endorsed for edexcel = Edexcel AS/A level BIOLOGY B ] Ann Fullick PEARSONPublished by Pearson Education Limited, 0 Strand, London WC2R ORL. ‘www pearsonschoolsandfecclleges co uk Copies of oficial specifications for all Edexcel qualifications may be found on the website vveww.edexcelcom Text © Ann Fullick ‘Exam-style questions © Pearson Education Limited Baited by Natalie Bayne and Jo Egré Designed by Elizabeth Amous for Pearson Education Limited ‘Typeset by Tech-Set Ltd, Gateshead (Oniginalilustrations © Pearson Education Limited 2015 Mlustrated by Tech-Set Lid, Gateshead and Peter Bull Art Suidio Cover design by Elizabeth Amoux for Pearson Education Limited Picture research by Caitlin Swain (Cover photo illustration © Science Photo Library/King's College London ‘The rights of Ann Fullick and Graham Hartland to be identified as authors ofthis work have been asserted by them in accordance with the Copyright, Designs and Patents Act 1988, First published 2008 ‘Second ecition published 2015 191817 16 10987654 British Library Cataloguing in Publication Data ‘A catalogue record for this book is available from the British Library ISBN 9781447001144 Copyright notice All rights reserved. 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Clinical ‘ophthalmology, 5, 577 (2011), Clinieal Ophthalmology by Society for Clinical Ophthalmology (Creat Britain) Reproduced with permission ‘of ove Medical Press Limited in the format Republish in a book via Copyright Clearance Center, Figure on page 203 from the front cover of the DEFRA publication "What nature can do for you’, hitps:/ ‘wwe gov.uk/ government/uploads/system/uploads/attachment_ {ata /fle/221097 pb 3897-nature-do-for-you pa, Published by the Depariment for Environment, Food and Rural Affairs. © Crown Copyright 2010; Figure on page 240 from http://uwwwabpischools, ‘orguk/ page/modules/breathingandasthma/asthma? cfzn, ABPL Resources for Schools, Association ofthe British Pharmaceutical Industry (ABPI) with permission, Text Article on page 32 fiom "Trehalose: an intriguing diseccharide ‘with potential for medical application in ophthalmology’. Clinical ophthalmology, 5, 577 (2011), Clinical Ophthalmology by Society for Clinical Ophthalmology (Great Britain) Reprocuced with permission of Dove Medical Press Limited in the format Republish in a book via Copyright Clearance Center, Article on page 106 adapted trom ‘Deadly Ebola virus “could spread globally” alter plane brings itto Nigeria’, Daily Mail 28/07/2014 (Nick Fagge). Daily Mail: Article on page 106 adapted from ‘Epidemiology and surveillance http://www, afro who int/en/ clusters-a-programmes/dpe/epidemic-a-pandemic- alert-and- response outbreak-nevis/4236-ebola-virus-disease-west- afrea-29-july-2014 him. © Copyright World Health Organization (WHO) ~ Regional Office for Arica. 2013. Al rights reserved. Article on page 106 from hip: /ww wales.nhsuk/sitesplus/888/ page/74508, Public Health Wales; Extact on page 146 adapted from ‘In vitro ferlisation’, Heinemann Library (Flick, A); Poetry con page 168 trom "Oxford Ragwor’ (Short, G), with permission from Anthony Short; Article on page 188 adapted from ‘Quagga rebreeding 2 success story, Farmer's Weekly (Harvey. K), © 2014 Fonner’s Weekly Magazine: Anicle on page 188 from ‘A vapid loas cf stipes: the evolutionary history ofthe extinct ouages’. September 2008 Volume: 1 Issue: 3 (Jennifer A. Leonard etal), Copyright © 2014, The Royal Society, Anicle on page 240 from hitp.// www. abpischools org uk/page/modales/ breathingandasthnna/asthma7, clin, ABP] Resources for Schools, Association of the British Pharmaceutical Industry (ABPI) with permission; Article on page 200 from Encyclopedia of Life Sciences, John Wiley & Sons, Lid (Turgor Prossure by Jeremy Prichard, University of Birmingham 2001) © 2001, John Wiley & Sons, Lid Reproduced with permission of Blackwell Publishing, ‘The Publisher would lke to thank Chris Curtis and Wade Nottingham {for their contributions tothe Maths skills section of this book. ‘The author would like to acknowledge and thank the teams at Science and Plants for Schools (SAPS), the Wellcome Trust Sanger Institute ‘and the ABPI for thei valuable input. The author would also like to thank the following for their support and individual contributions Dr Jeremy Pritchard: Alice Kelly: Amy Ekins-Coward: Tony Short ‘Wiliam Pulls Thomas Pulick: James Fulick, Eéward Pulick Chris Short Every effort has been madle to contact copyright holders of material reproduced in this book. Any omissions will be rectified in subsequent printings i notice is given to the publishersContents How to use this book TOPIC 1 Biological molecules 1.1 Chemistry for life 1 Chemistry for lie Exam-style questions 1.2 Biological molecules 1 1 Carbohydrates 1 ~ monosaccharides and. disaccharides 2 Catbchydrates 2 ~ polysaccharides 3. Lipids 4 Proveins Thinking Bigger Exam-style questions 1.3 Biological molecules 2 Nucleotides and ATP Nucleic acids How DNA works ‘The genetic code DNA and protein synthesis Gene mutation ‘zam-style questions 1.4 Enzymes 1 Emymes 2. How enzymes work 3 Enzyme inhibition Thinking Bigger Exam-style questions 6 10 14 16 18 at 25 28 32 34 36 38 42 47 50 52 54 56 58 62 64 66 TOPIC 2 Cells and viruses 2.1 Eukaryotic cells 1 Observing cells 2 Cell membranes 3 Eukaryotic cells 1 ~ common cellular structures 4. Bukaryotic cells 2 ~ protein transport 5 Eukaryotic cells 3 ~ plant cell structures 6 Bukaryotic cells 4 — plant organelles 7 The organisation of cells Exam-style questions 2.2. Prokaryotic cells 1 Prokaryotic cells 2 Viruses 3. Controlling viral infeetiona ‘Thinking Bigger Exam-style questions 2.3. Eukaryotic cell division - mitosis 1 The cell eycle 2 Mitosis 3 Asexual reproduction 4 Growth and repair ‘Thinking Bigger Exam-style questions 24. Meiosis and sexual reproduction 1 Sexual reproduction and meiosis, 2 Mutations 3 Gametogenesis, 4 Fentlsation in mammals and plants 5 Embryo development in mammals, ‘Thinking Bigger Exam-style questions 68 70 14 76 20 83 86 88 90 92, 94 98 102 106 108 ao 12 ana uur 120 122 124 126 128 132 135 140 143 148 148a TOPIC 3 Classification 3.1 Classification 32 33 1 Principles of classification What isa species? Identifying individual species New evidence for evolution Domains, kingdoms or both? ‘Thinking Bigger Exam-style questions Natural selection 1 2 3 4 Evolution and adaptation ‘Natural selection in action ‘The evolutionary race between pathogens and medicines Speciation ‘Thinking Bigger Examvstyle questions Biodiversity 1 2 3 4 ‘The importance of biodiversity Biodiversity within a species Beosystem services Ex-situ and in-situ conservation Examstyle questions 150 152 154 158 160 162 168 170 172 174 178 181 183 188 190 192 194 199 202 204 208 TOPIC 4 Exchange and transport aq 42 a3 aa Cell transport mechanisms 1 Trangpor in cells 2. Diffusion and facilitated diffusion 3. Osmosis ~a special case of diffusion 4 Active transport Exam-style questions Gas exchange 1 The need for gas exchange surfaces 2. The mammalian gas exchange system 3 Gas exchange in insects 4 Gas exchange in fish 5 Gas exchange in plants ‘Thinking Bigger Exam-style questions Circulation 1 Principles of circulation 2 The roles of the blood 3 Transporting oxygen and carbon dioxide 4 Blood circulation 5 The human heart 6 Controlling the heart 7 Atherosclerosis 8 Risk factors for atherosclerosis 9 Tissue fluid and lymph ‘Thinking Bigger Exam-style questions Transport in plants 1 Transport tissues in plants 2 The uptake of water by plants 3 Translocation of sucrose Thinking Bigger Exam-style questions Maths sills Preparing for your exams Glossary Index 210 212 214 216 220 222 224 226 228 232 234 236 240 242 244 246 248 250 254 257 260 263 266 270 272 274 276 278 281 287 290 292 294 300 306 316How to use this book ‘Welcome to your Edexcel AS/A level Biology B course. In this book you will ind a number of features designed to support your learning, Chapter openers Each chapter starts by setting the context for that haprer’s lernings + Link to other areas of Biology are shown. incuding previous knowledge tha isbult on inthe capex, fn tue earring that you wl cover ater in yur course + The All the maths you need checklist helps you 9 Yoon hat maths sls le equ Main content ‘The main part of each chapter covers all the points from the spectfication that you need to learn, The text is supported by diagrams and photos that will help you understand the concepts, Within each section, you will ind the following features: + Learning objectives at the beginning of each section, highlighting what you need to know and understand, + Key definitions shovm in bold and collated at the ‘end of each section for easy reference. + Worked examples showing you how to work through questions, and how your calculations should be set out, + Learning tips to help you focus your learning and avoid common errors. + Did you know? boxes featuring interesting facts to help you remember the key concepts. + Questions to help you check whether you have understood what you have just read, and whether there is anything that you need to look at again,Thinking Bigger “The book festures a number of Thinking Bigger spreads that give you an opportunity to ead and work with real Iie esearch and ‘writing abour science. The timeline atthe bottom of the spreads highlights which of the chapters the material relates to, These spreads will help you to + read realife material that’s relevant to your course + analyse how scientists write + think eitcally and consider the issues + develop your own writing + understand how diferent aspeets of your leaming piece together Exam-style questions ‘At the end of each chapter there are also exam-style questions [0 help you to: + test how filly you have understood the leaming + practise for your exams. Getting the most from your online ActiveBook ‘This book comes with 3 years’ access to ActiveBook* ~ an online, digital version of your textbook. Follow the instructions printed on the inside front cover to start sing your ActiveBook. Your ActiveBook is the perfect way to personalise your learning, as you progress through your Edexcel AS/A level Biology course. You can: + access your content onlin, anytime, anywhere + use the inbuilt highlighting and annotation tools to personalise the content and make it really relevant to you + search the content quickly using the index. Highlight tool Use this to pick out key terms or topics so you are ready and prepared for revision Annotations tool Use this to add your own notes, for example links to your wider reading, such as websites or other files. Ormake a note to remind yourself about work that you need to do. “For new purchases cay IF this access code has already been revealed may no longerbe val. If you have bought his testhock secondhand, the code may steady have been usec by te fist ner of the Bookwe % Chemistry for life ‘A alt spider Dolomedes fimbriatus sits on the surface of the water, hidden by the stems of water plants, waiting for the vibrations in the surface tension that alert her tothe presence of her prey. She is lage - up ta 23 mm actoss - yet water-repelient hairs enable her to run across the surfac her victims. These ae usually agus vital for this semiaquatic spider = and for ebrates that als live on or near the lite on Earth, er surface. Water is nit of life is the call, and un Biology isthe study of living things. The chemistry! The way atoms ace bonded together affects the way chemicals work int atfects everything, from the way plants make food by photosynthesis to the way your eyes respond to light In this chapter you will be looking at some ofthe key ways in which atoms and molecules interact to ‘make up the chemistry of life. You wil be using these basic principles the course, because they underpin the structures and functions of al the of ms you wil stud Around Jo-thitds ofthe surface of the Earth is covered in water and around two-thirds of your body is water. The oceans, rivers and lakes of the world are teeming with lifeand all the reactions in your cells take place in solution in water. In this chapter you will be applying your knowledge of the basic ‘chemical principles to help you understand just why war ie £0 vital for life Recognise and make appropriate use of units in calculation iNimetres) (eg, Use ratios (eg. representing the relationLife processes depend on molecules whose Punatieeenee Teed end eee eee Peat Eon eee eee eee rc Water is needed for photosynthesis Cee eae ene Pata ccd How carbohydrates, lipids and proteins are ere eriaed Cee eee) eee a ‘The importance of hydrogen bonding in the tertiary and quaternary structure of proteins and eee eter eres How waters taken into and moved around plants See an oes tissues and vessels in animal, plants and fungi Seta ey ‘The role of waterin the reactions of cellular co Perea er) NW irani cr Mau Ree Tied payer ence enn Creer ees bonding 3 See eer : Reeve irpreurenneter fineraerenries bare Saeed cae : eek ererte teehee mea Roe reer ne Teron Stet paperprereernesemreiy seri) . . Pieces Soe eee ae Ree ay tsChemistry for life By the end of this section, you should be able to.. © explain the role of inorganic ions in plants © explain the importance of the dipole nature of water in the formation of hydrogen bonds and ‘the significance of some of the properties of water to the organisms lonic and covalent bonding Biology isthe study of living things but ving tings are made up of chemical If you understand Some of the basi principles of chemistry you vil also develop a'mch beter understanding of biological systems, The chemical bonds within nd between molecls affect the properis ofthe compounds they form, Thsin tur affects the fonctions within te cell andthe orgasm, fig Ai i cependson some very fundamental chemistry The single basic unit ofall elements is the atom, When the atoms of two or more elements react they form a compound. An atom is made up of a nucleus containing postive protons and neutral neutrons surrounded by negative electrons, We model these electrons as orbiting around the nucleus in shells. When an atom has a full outer shell of electrons itis stable and does not react. However, ‘most atoms do not have @ full cuter shell of electrons, In chemical reactions, they are involved in changes that give them a stable outer shell. There are to ways they can achieve this: + Tonic bonding: the atoms involved in the reaction donate or receive eleetrons.‘The atom, or part of the molecule, gains one or more electrons and becomes a negative ion (anion). The other atom, of part of the molecule, loses one or more electrons and becomes a positive ion (cation). ‘Strong forces of attraction called ionic bonds hold the oppositely charged ions together game + +s» [i] Fa] an oa, ea ea {ig The formation of sadium chloride (salt an inorganic substance that is very important in ving organisms, an sample ofan bondi 10sr + Covalent bonding: the atoms involved in the reaction share electrons, Covalent bonds are very strong and the molecules formed are usually neural. However. in some covalent compounds, the ‘molecules are slightly pola'sed, The electrons inthe covalent bonds are not quite evenly shared. “This means the molecule has a part tha ssightly negative and a part that is slightly positive. This, separation of charge is called a dipole, and te tiny charges are represented as 6° and 6 (see fig D). “The molecule is described as.a polar molecule. This polarity is particularly common if ane or more hydrogen atoms are involved in the bond + He ——> HH (1) a) Q) hydrogen hydrogen hydrogen atom atom molecule © © © a Hot oH + Oe ae at ) } és) (2a) hycrogen hydrogen oxygen atom vrater molecule atom) ‘atom fig The formation ef hydrogen molecules and water molecules are examples of covalent bonding Be clear about the difference between ionic substances, charged particles and polar molecules. The importance of inorganic ions When ionic substances are dissolved in water the ions separate, Cells are 60-70% water and s0 in living organisms most onie substances exis: as postive and negative ions, Many ofthese ions play specialized role in individual ells ana inthe functioning of entire organisms. Here are some ofthe snorganic ions you vill meet as you sty biclogy, with an inciction oF one or mone oftheir roles Important anions + nitrate ions (NO;") ~ needed in plants for the formation of amino acids and therefore proteins from the products of photosynthesis, and also for the formation of DNA «+ phosphate ions (PO,?~) ~ needed in all living organisms including plants and animals in the formation of ATP and ADP as well as DNA and RNA + chloride ions (Cl+)— needed in nerve impulses and many secretory systems + hydrogen carbonate ions (HCO,”) — needed for buffering the blood to prevent it from becoming 100 acidic Important cations + sodium ions (Na*) — needed in nerve impulses and many secretory systems + calcium ions (Ca?) — needed for the formation of calcium pectate for the middle lamella between two cell walls in plants, and forbone formation and muscle contraction in animals + hydrogen ions (H)~ needed in cellular respiration and photosynthesis, and in numerous pumps and systems in organisms as well as pH balance “+ magnesium jons (IMg’)- needed for production of chlorophyll in plants uThe chemistry of water Water isthe medium in which all the reactions take place in living cells, Without it, substances could not move around the body ‘Waters one of the reactants in the process af photosynthesis, con which almost all life depends. And water is a major habitat = itsupports more life than any other part of the planet. Understanding the properties of water will help you understand rmany key systems in living organisms fig Water etal for fe on Earth in many aierent way ‘The importance of water 19 biological systems is due to the basie chemistry ofits molecules. The simple chemical formula of water isH,O. This tells us that two atoms of hydrogen are joined to cone atom of axygen to make up each water molecule (see fig F) However because the electrons are held closer to the oxygen ator than to the hycragen ators, water is a polar molecule. i N\A i 1045" {ig F Armedel ofa water molecule One of the most important results ofthis charge separation is that water molecules form hydrogen bonds. The slightly negative axygen atom of one water molecule wil attract the slightly positive hydrogen atoms of other water molecules in a ‘weak electrostatic araction called a hydragen bond. This means thatthe molecules of water ‘sick together’ more than you might otherwise expect, because although each individual hydrogen bond is weak. there area great many of them (as shown in fig G) Water has relatively high melting and boiling points eompared ‘with other substances that have molecules ofa similar siz — it takes more energy to overcome the attractive forges of all the hydrogen bonds. Hydrogen bonds are an important concept in biochemistry —for example they play an important part in protein structure (see Section 1.2.4) and in the structure and functioning of DNA (see Section 1.3.2) R figG Hydrogen bonding in water molecules. The importance of water ‘The properties of water make it very important in biological systems for several reasons + Water isa polar solvent. Because water i apolar molecule ‘many ionic substances lke sodium chioride will dissolve in it Mary covalently bonded substances are also polar and they +00 will dissolve in water although they often do not dissolve in other covalently bonded solvents such as ethanol. As a result most of the chemical reactions within cells occur in water (in ‘aqueous solution). + Water isan excellent transport medium because so many different substances will dissolve init, Water also carries other substances such as starch that form colloids rather than solutions. + As water cools to 4°C, it reaches its maximum density, As it cools further the molecules become more widely spaced, ‘Asa resul, ice is less dense than water and floats, forming an insulating layer and helping to prevent the water underneath it from freezing. Italso melts quickly because itis at the top, exposed to the sun. Itis very unusual for the solid form of chemical to be less dense than the liquid, but as a result ofthis ‘unusual property, organisms can live in water even in countries where it gets cold enough to freeze in winter + Water is slow to absorb and release heat ~ithas a high specific heat capacity. The hydrogen bonds between the molecules mean it takes a lot of energy to separate them. This means the temperature of large bodies of water such as lakes and seas does not change much throughout the year, making them good habitats for living organisms, + Water isa liquid and soit cannot be compressed. ‘This is an Jmportant factor in many lyeraulic mechanisms in ving organisms. + Water molecules are cohesive — the forces hetween the ‘molecules mean they tick together. This is very important for the movement of water from the rots to the leaves of plants.sr + Water molecules are adhesive ~ they are attracted to other different molecules. This is also Jmportant in plant transport systems and in surface tension. + Water has a vory high surface tension because the attraction berween the water molecules, including hydrogen bonds, is greater than the atraction between he water molecules and the air As a result the water molecules hold together forming a thin skin of surface tension. Surf sion is of great importance in plant transport systems, and also affects lf atthe surface of ponds, lakes and other water masses. fig wehout surace tension a rat spider could not move 1 How do ionic bonds and covalent bonds differ? 2. what are the ciferences between ini substances and polar substances? 3 How are ydrogen bonds formed between water molecules nd what eet do they have onthe proper ovate? 4. Te propenesef water fect ts lin ving organisms Discuss ‘Keydefinitions 0 ‘An anion isa negative ion, formed when an atom gains electron(s). ‘cation is a positive ion, formed when an atom loses electrons) lonic bonds are attractive forces between oppositely charged ions. Covalent bonds are formed when atoms share electrons. ‘A dipole isthe separation of charge in a molecule when the electrons in covalent bonds are not evenly shared. Apolar molecule is a molecule containing a dipole Hydrogen bonds are weak electrostatic intermolecular bonds formed between polar molecules Containing atleast one hydragen atom, BA Biology has 2 lot of application of scientific knowledge, so i's a ‘200d idea to remind yourself of the basics learnt at GCSE. 1 Remind yourself of ionic bonds by answering these questions, (2) Draw a diagram of a sodium ator, including the protons, neutrons and electrons, 2} (b) Draw 2 diagram of a chlorine atom, including the protons. neutrons and electrons, ia (c) Now show how sodium and chlorine atoms can be turned into sodium and chloride ions to form the ionic bond. [2] (Total: 6] 2 a) Draw one water molecule. ii (b) Using the atomic structure of oxygen and hydrogen, explain ‘hy the electrons are held closer to the oxygen atom. [2] (6) Explain how a molecule of sodium chloride can dissolve in water (3) [Total: 6] 3. Read through the following account about water. then write ‘on the dotted lines the most appropriate word or words to ‘complete the account Water molecules are described as. Se because they have a slight positive charge at one end of the ‘molecule and a slight negative charge atthe other end. This ‘makes water a good, for salts and substances such as sugars. Bonds that form between water molecules are called bonds. ‘Waters a good coolant because it has @ high sey which means that it takes a lot of heat to changeit rom a liquid to a gas. Water also has a high... which means that a lot of ‘energy is needed to cause a small rise inits temperature. [5] (Total: 5] Exam-style questions 4 Fill in this table to show which ion is used for which purpose. POF ca Needed to produce chlorophyll (4) (Total: 4} 5. There are many substances important to living organisms ‘These can be classified as A. cations B anions polar molecules D_ non-polar molecules Identity the following molecules using one of the terms above. (2) water (0) chloride ion (CI>) (c) sodium ion (Na*) {d) hydrogen carbonate ion {e) methane (phosphate fon (6) [Total: 6] 6 Acids release hydnogen ions (H") into solution. Explain how !hyimagen carbonate ions (HCO. act to prevent the Hood ‘becoming too acidkc. 2) (Total: 2} 7 {a} A.student wrote a tte to her table of results in a water based ink. and then underlined in ballpoint pen. Her lab partner then accidentally spilled water over the page. The tle smudge, but the underining dirt Using your nowledge of the properties of water explain these observations. (2] {b) Having done some research, the student decided that it would be more sensible ro do her tables of results using @ pencil, Use your knowledge of solvents to explain wy this 's 8 good idea @ (Total: 4)8 w (@) Draw the electron shells ofthe following atoms: (carbon (i) oxygen (i) sodium () argon 4) (&) Use the information from the electron shells to state how many protons each of the above elements has. (4) (6) Use the information of the number of protons to explain ‘why CHqis a non-polar molecule but HO isa polar molecule. a (@) Use the periodic table to find the relative atomic mass of ‘each element. Why is this number always bigger than the proton number? i) (€) Looking again atthe electron shells, explain why eaxbon ‘can form four bonds, oxygen can form two, sodium only forms one bond, but argon can form no bonds 4) [Total: 15] Marion wanted to build a pond to breed fish in the north of England. Temperatures inthis region can fall below 0°C in the winter She was advised to make sure the pond was at teast 3m deep and held 3500 00 res of water. Use your lrnowledge of the properties of water to explain why such a large pond was necessary 4) (Total: 4] Pond skaters are insects that can travel on the surface of water Using your knowledge of the properties of water, explain how these insects can travel ike this, By [Total: 3]A sivall child with a swollen belly sts istlesly inthe Caribbean sun. Like many millions of newy weaned infants she is suffering from kuashiorkor. She is ‘sugar baby - socalled because she isnot lacking in calories but in protein, A breastfed baby gets ll the carbohydrates, lipids and proteins it needs from its ‘mother’s milk. Butin many countries, the main foods used to wean babies are cereals. Cereals contain around 12-14% water, 65-75% carbohydrate, 2-6% lipids and 7-12% protein. In contrast, the human | body ie made up of arounc 64% water, 20% pratein, 10% fat, 1% carbohydrate and 5% minerals. Cells depend on proteins to work so ifthe diets severely lacking in protein, over time the health of the child (or adult al fal In this chapter you wil be studying some ofthe key biological molecules that make up the cells of you conn bedy, and those of other organisms. You will laokat carbohydrates, from the simplest sugars tothe ‘most complex polysaccharides, These molecules have a wide variety of uses in organisms, from the fuel for cellular respiration to the main structural material in plants. As you discover how the molecules are joined together you wil recognise the relationships between the structure ofthe molecules and their functions in the body. “The same links between structure and function are lear when you look at the way lipid molecules build up. B For example lipids are used as energy stores in bath animals and plants Lipids are non-polar molecules but ‘you will discover how they can become polar in combination with other inorganic groups such as phosphates. This polarity has great importance forthe characteristics ofthe cel membrane. Proteins are key molecules in cells both as part of the structure of the membranes and as the enzymes that contal the metabolism ofthe cell and the whole organism, Proteins are long chains of amino acids that are hheld together to make complex structures by chemical bonds, including the covalent bonds, ionic bonds and hydrogen bonds you discovered in Chapter 1.1 IR ecognise and make appropriate use of units in caeulations (eg nanometre) Use ratios (¢9, representing the eatonships Between atoms in an ion or molecule)Peet ard Sypgygeere Maine ere i fates Se ogra cae | rng ae seca rie have | studied before? eee ee ree od epee snd ee en ca Pent ur ene tee Ts een een puna Be cee cel eee ee eee ees Dn ee te aac How earbohyaratesand proteins actas signaling ee eee eet eae Sete eee ead eee el eee Pr ‘ ee ee ce EE eer et ete cian een ee eas eee ees > ns ee, ee ee) age ee amen) Want vaunted paren erevnestiaser ett] ts neers Se ny Hosalioanenetsporaueeritaer neh or et re ree ee ere eer renner Pee eee Se ee importanceas storage molecilesin plats and cts ester bonds +The structure ofamino acids peptides and Pec beo Tent mnn nity Ta Seen oceans os eres bee ever ant near eter eee ~SCarbohydrates 1 - monosaccharides and disaccharides By the end of this section, you should be able to.. © describe the difference between monosaccharides and disaccharides © describe the structure of the hexose glucose (alpha and beta) and the pentose ribose © explain how monosaccharides join to form disaccharides thraugh condensation reactions forming glycosidic bonds, and how they can be split through hydrolysis reactions © explain how the structure of glucose relates to its function fig Corbohy-ses a rmeleculesin planta ake ~ and they a What are organic compounds? Biological molecules ae the key tothe structure and function of living things. Biological molecules are olten organic compouns. Organic compounds all contain carbon atom, They also contain atoms of hyéragen, oxygen and, leas frequent trogen, sulfur and phosphorus, Mest of the material in your body that is not water is made up of these organic molecules. An understanding of why onganic molecues ae special il ep you to understand the chemistry of biological molecules inducing carbohydrates, lipids and proteins Each carbon atom can make four bonds and so it can join up with four other atoms. Carbon atom bond particulary strongly to other carbon atoms to make long chains, The four bands of a carbon ‘atom usually form a tetrehedral shape and this leads to the formation of branched chains, or rings, cor any number of three-dimensional (3D) shapes. In some carbon compounds small molecules (monomers) bond with many other similar units to make a very large molecule called a polymer. The ability of carbon to combine and make macromolecules (large molecules) isthe basis of all biological molecules and provides the great variety and complexity found in living things. , cee Sa plane of the paper two bonds This bond sticks out of the plane of the paper HHH H can be shown with corners chan meee ryeogns ignore MwA YY ormoreofenas: HH HH H fig A The bonds in a carbon atom havea complicate diagame we use one of everal dfenert ways Carbohydrates Carbohydrates are important in cells as a usable energy source. They are also used for storing ‘energy, and in plants, fungi and bacteria they form an important part of the cell wall. The best kn carbohydrates are sugars and starch, Suerase isthe white crystalline sugar familia to us all, while ‘glucose is the energy supplier in sports and health drinks, Starch is found in flour and potatoes. But the group of chemicals knowm as carbohydrates contains many more compounds, as you will discover‘The basic structure of all carbohyctrates is the same. They are ‘made up of carbon, hydrogen and oxygen. There are three main groups of carbohydrates with varying complexity of molecules: monosaccharides, disaccharides and polysaccharides, Monosaccharides - the simple sugars Monosaccharides are simple sugars in which there is one oxygen ‘atom and two hydrogen atoms for each carbon atom present in the molecule, A general forrnula for this can be written (CH.O), Here n can be any number but it is usually low: + Triose sugars (n=3) have three carbon atoms and the molecular formula CsH,O:, They are important in the ‘mitochondria, where glucose is broken down inta triose sugars during respiration. + Pentose sugars (n=5) have five earbon atoms and the ‘malecular formula C:H,0;, Ribose and deoxyribose are Jmportant in the nucleic acids deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), vhich make up the genetic ‘material (see Sections 1.3.1 and 1.3.2), + Hexose sugars (n=6) have six carbon atoms and the molecular formula C:H.,O,. They are the best known monosaccharides. often taste sweet and include glucose, galactose and fructose. Molecular formulae show you how many atoms there are in the ‘molecule, and what type they are, but they do net tell you what the molecule looks like and way it behaves asit does. To show this you can use displayed formulae, Although these do not fallow ‘every wiggle and kink in the earbon chain, chey can give you a good idea of how the molecules are arranged in three dimensions. ‘This can reveal all sorts of secrets about why biological systems behave as they do (see fig D). ribose CHOH OH As | a \ ~ I dy figD Howse sugarshavea hese crainscan make a significant ference othe way imwhich the molecule can be used by the body Werumber the carbon ators 30 = can denafy the diferent arangements og truce. The arrangement te aloms on a-glucose and f-glucose Glucose comes in different forms (isomers), including a-giucose and -glucose. These two isomers result from different arrangements of the atoms on the side chains of the molecule (see fig E) ‘The afferent isomers form cifferent bands between neighbouring ‘glucose molecules, and this affects the polymers that are made. ex-glucose Begiucese (chon HOH HY Q mh 4. EH } > Ce Ho 7 HHO H OH or even more simply: av-glucose H, H. HO Xs HO In these diagrams, the positions of carbon atoms are represented by their numbers only Note carefully he different arrangernent of atorns around the carbon 1 atom in aeglicose and B-glucose, fig The difrence in suture becusen a-ucose and fg siall, bu ithas a big impact onthe function ofeach molecule Did vou know? Hydrogenating some sugars reduces the energy they provide. When slucase is hydrogenated it forms sorbitol (C,H, 0). Sorbital tastes Lp to 60% sweeter than glucose but it provides less energy when is used in the body (11 Kg" compared to 17klg"). The combination of the very sweet taste and the lower energy count makes it useful as a sweetener for people who want to lose weight. small change in the chemical structure has abi effect on function. Disaccharides - the double sugars Disaccharides are made up of two monosaccharides joined together ~ for example sucrose (ordinary table sugar) is formed bby a molecule of a-glucose joining with a molecule of fructose. ‘Two monosaccharides join in a condensation reaction to form a disaccharide, and a molecule of water (H,O) is removed. “The link between the two monosaccharides results in a covalent bond known as a glyeosidie bond (see fig F). We use numbers to show which carbon molecules are involved in the bond, If carbon 1 on one monosaccharide joins to carbon 4 on another ‘monosaccharide, we call ita 1.4-giycosidic bond. If the bond is bbetiveen carbon | and carbon 6, its a 1.6-glycosidic bond. 19orglucose a-glucose HY pou feo on Hi Y bund of “OH ‘condensation yoo a: 1h H wo SSN 1 delycosidic bond fig The formation glycoside b condensation reaction betwen two monosaccharides results na dsacchatide anda molecule cl water When different monosaccharides join together different disaccharides result. Many disaccharides taste sweet. Petree eet sucrose stored in plants such as arglucose + sugar cane uctose lactose milk isthe man | erglucose + carbohy yund in ile maltose malt sugar ~ found in germinating seed such as barley table A [hres common dieacsnandes Did you know? Testing for sugars + Benedict solution isa chemical test for reducing sugars. Itisa bright blue solution thet contains capper) ans Some sugars react resdiy with this solution when heated gently and reduce the copper() ions to copper} ions, forming a precipitate and giving a colour change from biue to orange. They are known as reducing sugars. All ofthe monosaccharides and some disaccharides are reducing sugars, + Some sugars do not react with Benedict solution, They are known as non-reducing sugars. You can heat a non-reducing sugar such as sucrose with afew drops of hydrochloric acto hydrolyse the ycosidic bonds. Allow it to cool and then neutralise the solution With sodium hydrogen carbonate. This produces the monosaccharide Units ofthe sugar, which wil now give a positive Benedict test. fig Benecic’ tet for reducing sugars 20 ‘| What are the properties of organic compounds that make them so Important iving organisms? 2 pescrvehowa ghcsiicbondistormed beween two Imonosecharie orm a saccharide Keydefinitions ‘Amonomer isa small molecule thats a single unit ofa larger molecule called a polymer polymers along chain molecule made up of many smaller, repeating monomer units joined together by chemical bonds. -Amacromolecule isa very large molecule often formed by polymerisation. Starch sa long chain polymer formed of a-glucose monomers. Sucrose isa sweet tasting disaccharide formed by the joining of ce-glucose and fructose by a glycosidic bond. Glucose isa hexose sugar ‘Amonosacchatide isa single sugar monomer. ‘disaccharides a sugar made up of two monosaccharide units joined by a glycosidic bond, formed in a condensation reaction ‘A polysaccharide is a polymer made up of long chains of monosaccharide units joined by glycosidic bonds [Atriose sugars a sugar with three carbon atoms. [pentose sugar isa suger with five carbon atoms Ribose isa pentose sugar that makes up part ofthe structure of RNA. Deoxyribose sa pentose sugar that makes up part ofthe structure of DNA. Deoxyribonucleic acid (ONA) isa nucleicacidthatactsas the genetic material in many organisms. Ribonucleic acd (RNA) sa nuceic acid which can actas the genetic material in some organisms and is involved in protein synthesis Alhexose sugars a sugar with siccarbon atoms. Isomers are molecules that have the same chemical formula, but different molecular sructures ‘Acondensation reaction isa reaction in which a molecule of water is removed from the reacting molecules asa bond isformed between them glycosidic bond isa covalent bond formed between two monosaccharides in condensation reaction Reducing sugars are sugars that react with blue Benedict’ solution and reduce the copper(I) ions to copper ons giving an orangey: red precipitate. Non-reducing sugars are sugars that do not react with Benedict’ solution.Carbohydrates 2 - polysaccharides By the end of this section, you should be able to... ‘© explain how monosaccharides join to form polysaccharides through condensation reactions forming glycosidic bonds; and how these can be split through hydrolysis reactions © explain how the structure of polysaccharides relates to their functions The most complex carbohydrates are the polysaccharides. They are made of many monosaccharide units joined by condensation reactions that form glycosidic bonds (see Section 1.2.1, fig F), Molecules with 3-10 sugar units are known as oligosaccharides, wiile molecules containing 11 or Remember that glycosidic more monosaccharides are known as true polysaccharides Polysaccharides do not have the sweet bonds are formed withthe taste of many mono- and disaccharides, but these complex polymers form some very important removal of a molecule of water iiolegieal molecules in condensation reactions and broken withthe addition of a nakes them ideal as storage molecules: molecule af water in hydrolysis reactions The structure of polysaccha + They can form very compact molecules, so large numbers can be stored ina cel + The glycosidic bonds are easily broken, allowing rapid release of monosaccharide units for celular respiration. + They are not very soluble in water so have litle effect on water potential within a cell and cause ‘no esmotic water movement The glycosidic bond between two monosaccharides is split by a process known as hydrolysis, {see fig A). The hydrolysis reaction is the opposite of the condensation reaction that formed th ‘molecule, so water is added to the bond, Polysaccharides are gradually broken dow into shor shorter chains and eventually single sugars are lef. Disaccharides break down to form two and monosaccharides. Hydrolysis takes place during digestion in the gut, and also in the muscle and lve cells when the carbohydrate stores are broken down to release sugars for use in cellular respiration a-glucose a-glucose } 0, 1 ut \ HH stein | mon, HO ROY OHH H Ho ° ‘OH maltose ~I.t-ycosiic bond fig Gycosicic bonds a ade by condensation reactions and broken down by hydolss aDidyouknow? __ Testing for starch Ifyouadd afew drops of reddish-brown iodine solution toa solid sample ora sample Insolution, when starch is present the solution will un 4 blue-biack, 22 sa Carbohydrates as energy stores Starch Starch is particulary important as en energy store in plants The sugars produced by photosynthesis are Tape convertedinte starch, wich sinsohble and compact but canbe broken dlown rapidly to release glucose wien is needed. Storage organs such a potatoes ae pacar tichin starch ‘Starch is made up of long chains of e-glucose. But if you look at it more elosely you will see that it is ‘actually a misture of two compounds: Amylose: an unbranched polymer made up of between 200 and 5000 glucose molecules As the chain lengthens the molecule spirals, which makes it more compact for storage. Amylopectin: a branched polymer of glucose molecules. The branching chains have many terminal glucose molecules that can be broken off rapidly when energy is needed. Amylose and amylopectin are both long chains of a-glucose molecules — so wy are the molecules, 0 different? It all depends on the carbon atoms involved in the glycosidic bonds Amylose is made up purely of exglucose molecules joined by 1.4-glycosidic bonds, which is way the ‘molecules are long unbranched chains. In amylopectin many of the glucose molecules are jeined by 1.4-glycosidic bonds, but there are also afew L.6-glycosidic bonds. This results inthe branching chains that change the properties of the molecule, So starch has a combination of straight chain amylose and branched chain amylopectin ‘molecules. This combination explains why carbohydrate foods lice pasta are so good for you. ‘when you are doing sport. The amylopectin releases glucose for cellular respiration rapidly ‘when needed. Amylose releases glucose more slowly ever @ longer period, Keeping you going longer side group amylose 3 xy [os cchain forms a spiral cooondonnn amylopectin oS tO seas tai We 1 drglycosidiec took —S ° fig Amylose and amylopectin - a smal ference in the postion ofthe glycosidic bonds inthe molecule makes a big liference tothe propories ofthe compound.Glycogen Glycogen is sometimes referred to as ‘animal starch’ because itis the only carbohydrate energy store found in animals (see fig C). Its also an important storage carbohydrate in fungi ‘Chemically, glycogen is very similar to the amylopectin molecules in starch, and is also made up of many a-glucose units Like starch, its very compact, but the glycogen molecule has more 1,6-lycosidic bonds, giving it many side branches. As a result, glycogen can be broken down very rapidly: This makes it an ideal source of glucose for active tissues with a constantly high rate of celular respiration, such as muscle and liver tissue Carbohydrates in plants Polysaccharides ar very important in plants, Starch isthe main eneigy storage material in plants Atypical tarch grain in a plant tel contains 70-20% amylopectin, withthe rest beng amylose {a) starch grains ina plant cell (b) glycogen granules in liver cells fig€ Storage carnonycrates in plant and animal cals Cellulose is an important structural material in plants, The cell ‘wall (see Section 2.1.8) is an important feature that gives plants ‘their strength and support It is made up langely of insoluble cellulose. Cellulose has much in common with starch and _slycogen. It consists of long chains of glucose joined by glycosidic bonds. However, as you will remember there are two structural isomers of glucose, a-glucose and f-glicose, In starch, the monomer units are aeglucose. In cellulose, they are B glucose and are held together by 14-glycosidic bonds where ‘one of the monomer units has to be turned round (inverted) s0 the bonding can take place. Ths linking of -glucose molecules, means thar the hydraxyl (-OH) groups stick out on both sides of the molecule (see fig D). This means hydrogen bonds can pony form berween the partially positively charged hydrogen atoms of ‘the hydroxy] groups and the partially negatively charged exygen atoms in other areas of the glucose molecules. This is knowin as cross-linking and it holds neighbouring chains firmly together Many of these hydrogen bonds form, making celiulose a material ‘with considerable strength, Cellulose molecules do not coil or spiral - they remain as very long, straight chains. In contrast, starch molecules, with L4- and 1,6-glycosidic bonds between, ‘eeglucose monomers, form compact globular molecules that are ‘useful for storage. Beshucose Prglucose # OOH B. OOH HO! HHO H H OH Hi H HO! HOW ‘OH condensation lass x Hot HO O H “SX : HO. xX HO, 0, anes 2 XX Pro i fay ve OH KX, hydrogen bonds fig Calulose molecules consist of @ glucose moromes joined together by “egyczsidc bonds, ‘This difference in structure between starch and cellulose ‘gives them very different properties and functions, Starch is an important source of energy in the diet for many animals However, most animals do not possess the enzymes needed to break the 1,4-glycosidie bonds between the molecules of Beglucose and so they cannot digest cellulose. Ruminants such as cows and sheep, have bacteria, fungi and protozoa living in their _gut which produce cellulose-digesting enzymes. Itis the cellulose in plant food that acts as roughage or fibre in the human diet ~ an important part of a healthy diet even though you cannot digest it 2B24 Be clear about the diferences between a glucose and glucose and between 1L4-glycosidic bonds and ‘e-glycosidic links ~ is easy toiget them wrong and lose marks asa resut. at Explain how the structure of carbohydrates is rlated to their function as storage molecules providing the fue for cellular respiration in animals and plants, 2. Explain how the chemical structure of cellulose differs from that of starch and how this affects the way they can be used to supply enezgy in animals. IDR, ty ° HO, 2 38 xx cellulose ‘Oligosaccharides are molecules with 3-10 monosaccharide unis Hydrolysis ia reaction in which bonds are broken by the addition of a molecule of water. “Amylose isa complex carbohydrate containing onty glucose monomers joined together by 14- glycosidic bonds o the molecules form long unbranched chains. Amylopectin isa complex carbohydrate made up of glucose monomers joined by both 1,4-glycosidic bonds and I,6-glycosidic bonds so the molecules branch repeatedly Glycogen is made up of many «glucose unis joined by 1,4glycosidic bonds but also has 1/S-lycosidic bonds, giving it many side branches. Cellulose is 2 complex carbohydrate with fglucose monomers held together by 1-glycosidic bands. is very important in plant cel walBy the end of this section, you should be able to... ‘© explain the synthesis ofa triglyceride, including the formation of ester bonds during condensation reactions between glycerol and three fatty acids © describe the differences between unsaturated and saturated fatty acids ‘© explain how the structure of lipids relates to their role in energy storage, waterproofing and insulation © explain the structure and properties of phospholipids in relation to their function in the cell membranes. The lipids are another group of organic chemicals that play a vital role in organisms. They form an integral part of all cell membranes and are also used as an energy store. Many plants and animals cconwert spare food into oils or fats to use when they are needed. For example, the seeds of plants contain lipids to provide energy for the seedling when it starts to grow, which is why seeds are such {an important food source for many animals. 4 4 Fats and oils | | Fats and ol are important groups of lipids Chemical they ar extremely simi but ats suchas. HCCC (eee ar omen ok aateunlcopatiget he Glas pe | oneal meal Hp ie a fetal ler cea ej re ue co ety en gropnrion nf. cnr tan entobyrmaes: tsae 9 nares oc OH OM OH {poe bes ri, Aly Asa ad gifcee ris 1h Tey mu carmn Tey dew orpupsltemlectare presente Gioved kaa ic dlcnied teense, ake neeoaess Ally acids have along hydrocarbon chain a plated backbone ofcatbon atoms wth hydrogen atoms attached, a carboxy group (-COOH) at one end. Living tissues contain more than 70 different kinds of fatty acids. Fatty acids vary in two ways: + The length of the carbon chain can differ (although often 19-17 carbon atoms long in organisms) + The fatty acid may be a saturated fatty acid or unsaturated fatty acid [na saturated fatty acid, each carbon atom is joined to the one next co it by a single covalent bond, A common example is stearic acid (see fig B). In an unsarurated fatty acid, the carbon chains have ‘one or more double covalent bonds in them. A monounsaturated fatty acid has one double bond anda polyunsaturated fatty acid has more than one double bond (see fig C). Linoleic acid is an ‘example of a polyunsaturated fatty acid. Itis an essential fatty acid in our diet because we cannot make it from other chemical cH, (cH), coor fg 8 Displayed formula of stearic acid, a satura 2526 fig Displayed formula of nolec a Forming ester bonds AA fator oil results when glycerol combines with one, twa or three fatty acids to form a monoglyeeride, a diglyceride or a triglyceride. A bond is formed in @ condensation reaction between the carboxyl group (COOH) of a fatty acid and one of the hydroxy! groups (-OH) of the glycerol. A molecule of water is removed and the resulting bond is known as an ester bond. This type of condensation reaction is, called esterification (see fig D). The nature of the lipid formed depends on which fatty acids are present, So, for example, lipids containing saturated fatty acids are more likely to be solid at room {temperature than those containing unsaturated fatty acids For simplicity faty acids are represented by this general ° formula where represents the hydrocarbon chain The faty acids below are drawn in reversed form, R—C—OH glycerol 3 fatty acids triglyceride o lester bond, 9° 30) H o: I OH HOMC—R < hydrolysis H—C—oH HO-C—R <— © condensation H—C—OH HOLC—R K #H Note: there are only 6 ators of. ‘oxygen in a triglyceride molecule fig Formation of este The nature of lipids Lipids contain many caborhydogen bonds and ite cxygen. When iis are oxidised in respiration, the bonds are broken and cabo dioxide and water are the ultimate products. This reaction canbe used to dive the production of lt of ATP (ee Section 1.3.1) Lcies, especially triglycerides, store about thee times as mach energy asthe same mas of carbohydrates ‘The hydrophobic nature of lipids is @ key feature of their role in waterproofing organisms. Oils ae ‘important in waterproofing the fur and feethers of mammals and birds, wile insects and plants use waxes for waterproofing their outer surfaces (see fig B). Lipids are good insulators fatty sheath insulates your nerves 50 the electrical impulses travel faster They also insulate animals against heat loss — the thick layer Of blubber in whales isa good example. Lipids have a very low density, so the body fat of water marnmals ‘helps them to float easily All lipids dissolve in organic solvents, but are insoluble in water, so lipids do not interfere with the many water-based reactions that go on in the cytoplasm of a cell (@) (b) fig Ol onthe fatness, nthe sua af hess png leaves makes them very watrprcotPhospholipids Inorganic phosphate ions (-PO,) are preset in the cytoplasm of every cell Sometimes one of the yeas groups oF aycee) undergoes an esterification reaction witha phosphate group instead of with fatty acid and a simple phospholipids formed, Phospholpi are important because te lp ane the phosphate pars ofthe molecule get very diferent properties “The fatty acid chains of a phospholipid are neutral and insoluble in water In contrast the phosphate head carries a small negative ‘charge and is soluble in water When these phospholipids come into contact with water the two parts of the molecule behave differently The polar phosphate partis hydrophilic and cissolves readily in water (sce fig F). The lipid tails are hydrophobic, so they do not dissolve in water Ifthe molecules are tightly packed in ‘water they either form a monolayer, with the hyrophilic heads in the water and the hydrophobic lipid tails in the air or clusters called micelles. In a micelle. all the hydrophilic heads point ‘outwards and all the hydrophobic tals are inside (see fig G) hydrophilic head hydrophobic tall fig phospholipid hydrophobic air end ‘aqueous hydrophilic ~~ solution sy fig Phospholipids form 2 mo ‘A phospholipid monolayer may form ata surface between air and ‘water but this isa feisty rare situation in living cells where there {are water-based solutions on either side of the membranes. With ‘water on each side, the phospholipid molecules form a bilayer with the hydrophilic heads pointing into the water protecting the hydrophobic tas in the middle (see fig H).‘Thisstructure, the unit ‘membrane, isthe bass of all membranes aqueous solution Phosphate heads move hesphate head oyands aqueous solution “hydrophilic phospholipid aqueous solution of all mem fig Alpi bilayer ithe boc ‘| Describe the main difference between a saturated and an ‘unsaturated lipid, and the effect of ths difference on the properties, ofthe lipids. 2 explain how ghee are fou Key definitions Lipids are a large family of organic molecules that are important in cell membranes and as an energy store in many organisms, They include triglycerides, phospholipids and steroids. Alatty acid is an organic acid with along hydrocarbon chain. Giycerol is propane-1.23-triol, an important component of triglycerides [An ester bond is a bond formed in a condensation reaction between the carboxy group (-COOH) of a Fatty acid and one of the hydroxy groups (-OH] of glycerol ‘saturated fatty acid isa fatty acid in which each carbon atom is joined tw the one next to it nthe hydrocarbon chain by asngle covalent bond. [An unsaturated fatty acid is fatty acid in which the carbon atoms in the hycracarbon chain have one or more double covalent bondsin them. ‘A monounsaturated fatty acid is fatty acid with only one double covalent bond between carbon atoms in the hydracarbon chain, ‘polyunsaturated fatty acid is. fatty acid with two oF more double covalent bonds between carbon atoms in the hydrocarbon chain, Esterfication is the formation of ester Bonds phospholipid isa chemical in which glycerol bonds with two fatty acids and an inorganic phosphate group, Hydrophilic molecules dissolve readily in water. Hydrophobie molecules will not cissolve in water Amonolayer isa single closely packed ayer of atoms or molecules. [Armicelle isa spherical aggregate of molecules in water with hydrophobic areas in the mide and hydrophilic areas outside Abilayer isa double layer of closely packed atoms or molecules, ‘Aunit membrane i a bilayer structure formed by phospholipids in an aqueous environment, with the hydrophobic tailsin the middle and the hydrophilic heads on the outside. 27Proteins By the end of this section, you should be able to.. © outline the structure of an amino acid © explain the formation of polypeptides and proteins and the nature of the bonds in proteins © explain the significance of the primary, secondary, tertiary and quaternary structure of protein in determining the properties. of fibrous and globular proteins © explain how the structure of collagen and haemoglobin is. related to their function About 18% of your body is made up of protein. Proteins form hrar, skin and nails, the enzymes needed for metabolism and digestion, and many of the hormones that control various body systems, They enable muscle fibres to contract, form antibodies that protect you from disease, help clot your blood and transport ‘oxygen in the form of haemoglobin, Understanding the structure of proteins helps you develop an insight into the detailed biology of cells and organisms, Like carbohydrates and lipids, proteins contain carbon, hydrogen and oxygen. In addition they all contain nitrogen and many proteins also contain sulfur Proteins are another group of macromolecules made up of many small monomer units called amino acids joined together by condensation reactions, Amino acids combine in long chains to [produce proteins, There are about 20 different naturally occurring amino acids that can combine in different ways to form a vast range of different proteins. Amino acids ‘All amino acids have the same basic structure, which is represented as a general formula. There is always an amino group (-NH,) and a carboxyl group (COOH) attached to a carton atom (see fig A), The group known as the R group varies between amino acids. This is where sulfur and selenium are found in the structure of a few amino acids. The structure of the R group affects the way the amino acid bonds with others in the protein, depending largely on whether the R group is polar or not general formula R ‘This pat is como the examples blow. slyeine cysteine H cH, sit fig A. Some ciferenc amino acids. In te simpos amino aie gcine Risa single hydrogen atom, ina larger amine aca such a eystelne, Ris muc 28 Forming proteins from amino acids Amino acids join together by 2 reaction between the amino group Cf one amino acid, and the carbaxy/ group of another They join in a condensation reaction and a molecule of water is ost A peptide bond is formed when two amino acids jon and a dipeptide isthe result (see fig B)."The R group isnot involved inthis reaction, Mor land maze amino acids join to form polypeptide chains which contain from a hundred to many thousands of arn acids. When the polypeptide folds or coils or associates with other polypeptide chains it forms @ protein. amino acid 1 amino acid 2 (inverted) H HO N Ry condensation |) hydrolysis 0 So Ry H HO H bobo H—N—C—CwwN—C—C—OH a I Peptide HOH OO PRS Ry dipeptide fig Amino acid pide bones King blocks of proteins jon Bonds in proteins The peptide bond between amino acs isa strong bond, Other bonds also form between the aminoacids ina chain o form the 30 Sartre ofthe protein, They depend onthe atoms in he group and include hydrogen bonds disulfide bonds end ionic bonds Hydrogen bonds in amino acids, tiny negative charges are present on the oxygen cf the carboxyl groups and tiny positive charges are present on, the hydrogen atoms of the amino groups. When these charge ‘groups are close to each other, the of forming a hydrogen bond, Hydrogen bonds are weak, but they ‘can potentially form between any two amino acids positioned correctly so there are lots of them holding the protein together very firmly. Hydrogen bonds break easily and reform if pH or ‘temperature conditions change. They are very important in the folding and coiling of the polypeptide chains (see fig C). pposite charges attractDisulfide bonds Disulfide bonds form when two cysteine molecules are close together in the structure of a polypeptide (see fig C). ‘An oxidation reaction takes place between the two sulfur containing groups, resulting in a strong covalent bond known asa disulfide bond. These disulfide bonds are muuch stronger than hydrogen bonds, but they occur much less often. They are ‘important for holding the folded polypeptide chains in place. B pleated sheet av-helix fig Hydrogen bond and dude bonds maintain the shape of protein moles and this determines ther uncron lonic bonds [onic bonds can form between some of the strongly postive and negative amino acid side chains found buried deep inthe protein molecules, Those links are known as salt bridges, They are strong, bonds, but they are not as common as the other structural bonds, figD Straightening your so the hair curs ina diferent ramon sgement ofthe hygen bonds Your hair is made of the protein keratin. Some methods of styling the hair actually change the bonds within the protein ‘molecules. Blow drying or straightening your hair breaks the Iydrogen bonds and reforms them with the hair curling in a different way temporarily until the hydrogen bonds reform in their original places. Perming breaks the disulfide bonds between the polypeptide chains «and reforms them in a different place. This effect is permanent — your hair will stay styled in that particular way unt itis cut Protein structure Proteins can be described by their primary, secondary, tertiary and ‘quaternary structure (see fig E) + The primary structure of a protein is the sequence of amino acids that make up the polypeptide chain held together by peptide bonds + The secondary structure of a protein is the arrangement of the polypeptide chain into a regular, repeating structure, held together by hydrogen bonds. One example isthe right-handed helix (a-helix), a spiral col with the peptide bonds forming the backbone and the R groups sticking out in all directions Another is the f-pleated sheet, in which the polypeptide chain, folds into regular pleats hele together by hydrogen bonds between the amino and carboxyl ends of different amino acids. Most fibrous proteins have this sort of structure, Sometimes there is no regular secondary structure and the polypeptide forms a random call + The tertiary structure is a evel of 3D organisation imposed on top of the secondary structure in many proteins The amino acid chain, incuding any a-helices and A-pleated sheets, is folded further into complicated shapes. Hydrogen bonds, disulfide bonds and ionic bonds between amino acids hold these 3D shapes in place (see page 30). Globular proteins are an example of tertiary structures. + The quaternary structure of a protein is only seen in proteins consisting of several polypeptide chains, The quaternary structure describes the way these separate polypeptide chains fit together in three dimensions. Examples include some very important enzymes and the blood pigment haemoglobin. ‘The bonds that hold the 3D shapes of proteins together are affected bby changes in conditions such as temperature or pH. Even small changes can cause the bonds to break. resulting inthe loss of the 3D shape of the protein, We say thatthe protein is denatured. [Because the 3D seructure of these proteins is important ta the way they work, changing conditions inside the body can cause proteins such as enzymes to stop working propery. Primary structure — the linear sequence of amino acids in a peptide. BBE PO PD Pe Secondary structure ~ the repeating pattern in the structure of the peptide chains, such as an ce-helix ar B-pleated sheets, Tertiary structure secondary structure, the three-dimensional folding of the Be (Quaternary structure ~ the thrze-dimensional arrangement of more than one tertiary polypeptide. fig The 30 stucture of proteins 29Fibrous and globular proteins Fibrous proteins “The complex structures of lage protein molecules relate closely to their functions inthe body. Fibrous proteins have lite or no tertiary structure. They are long, parallel polypeptide chains with cccasional croselnkages that form ito flares. They are insoluble in water and ate very Lough, which makes them ideally suited to their structural unetions win organisms. Fibrous proteins appear inthe structure of connective tise in tendons and the ‘matrix of bones, in the structure of muscles asthe silk of spiders’ ‘webs and sileworm cocoons, and as the Kerstin that makes Up hai nail, hos and feathers. Collagen isa fibrous protein that gives strength to tendons, ligaments, bones and skin. It isthe most common structural protein found in animals — up to 35% of the protein in your body is collagen. Collagen is extremely strong ~ the fibres have a tensile strength comparable to that of steel. This is due to the unusual structure of the collagen molecule. Its made up of three polypeptide chains, which are each up to 1000 amino acids long, The primary structure of these chains is repeating ‘sequences of giycine with two other amino acids - often proline and hydroxyproline, The three a-chains are arranged in a unique triple helix, held together by a very large number of hydrogen bonds. These collagen molecules, which can be up to several millimetres long, are often found together in fibrils that in turn are hheld together to form collagen fibres. Collagen fibres are found combined with the bone tissue. giving ittensile strength rather like the steel rods in reinforced concrete, Inthe genetic disease osteogenesis imperfecta, the collagen triple helix may not form properly. The bone lacks tensile strength as & result, and itis brittle and breaks very easily. _Geusia Ren i seu er escrton a seme AMM i Pcusar Procolages Coban r fon (@bleles mole (ule eb Caagen Cag tre ea) fig Collagen sa ibrous protein of wth an unusual ple heicsucure and Globular proteins Globular proteins have complex tertiary and sometimes quaternary structures. They fold into spherical (globular) shapes. The large size of these globular protein molecules affects their behaviour in water 30 Because thei carboxyl and amino ends give them ionic properties yyou might expect them to dissolve in water and form a solution. In fact the molecules are so big that instead they form a colloid, Globular proteins play an important role in holding molecules in position in the cytoplasm. Giobular protein ae aso important in your immune system — for example, antibodies ae globular proteins Globular proteins form enzymes and some hormones and are involved in maintaining the structure of the eytoplasm (see Section 1.4.1 for details of proteins as enzymes) Haemoglobin is one of the best known globular proteins Itisa very large molecule made up of 574 amino acids arranged in four polypeptide chains which are held together by disulfide bonds. ach chain is arranged around an iron-containing haem group Hoemogicbin is « conjugated protein as vell as a globular protein, [tis the iron that enables the haemoglobin to bind and, Telease oxygen molecules, and itis the arrangement of the polypeptide chains that determines how easily the oxygen binds or in released (see Section 4.3.3) Conjugated proteins Some protein molecules are joined vith or conjugated ro another rmolecile called a prosthetic group. Ths strucaral change tsually affects the performance anc functions of te molecules You have already looked at haemoglobin, a large protein with an iron-containing prosthetic group Chloropyl the molecule involved in the eapture of light energy in photosynthesis, is another conjugated protein, with a prosthetic group that contains magnesium, Glycoproteins are proteins with a carbohydrate prosthetic group, ‘The carbohydrate part of the molecule helps them to hold on toa lot of water and also makes it harder for protein-digesting ‘enzymes (proteases) to break them down. Lots of lubricants used by the human bedy ~ such as mucus and the synovial uid in the joints ~ are glycoproteins waose water-nclding properties make them slippery and viscous, which reduces friction. This also helps to explain wity the mucus produced in the stomach protects the protein walls from digestion Lipoproteins are proteins conjugated with lipids and are very important in the transport of cholesterol in the blood. The lipid part Of the molecule enables it © combine with the lipid cholesterol "There are two main forms of lipoproteins in your blood ~ low- ensity lpoproteins (LDLs) (around 22 nm in diameter) and high- ensity lipoproteins (HDLs) (around &-L1 nmin diameter). The DLs contain more protein than LDLs, which is partly why they are denser ~ proteins are more compact molecules than lipids. Remember that amina acids are joined together by peptide bonds to form dipeptides and then polypeptides, but the 40 strutures of proteins are the result of hydrogen bonds, disuifide bonds and ionic bonds between amino acids within the polypeptide chainsTesting for protein To test forthe presence of protein, ether add 5% (w/) potassium or sodium hydroxide solution and 1% (w/v) copper sulfate solution, or Biuret reagent which isthe two chemicals ready mixed. When the Feagent/s are added to a test solution, a purple colour indicates the presence of protein 1. Explain how the order of amino acids ina protein affects the structure of the whole protein, 2 tydrogen bonds are weaker than dilide hands and ionic alt bridges, but they playa much bigger role in maintaining protein structure. Why sts? 3. The boy ues mary resources to maintain aelatvely consantintemal envionment With reerence to proves apan wy constant neal conders arse important “Amino acids are the buliding blocks of proteins, consisting ofan amino group (-NH,) and a carboxyl ‘group (COOH) attached to acarbon atom and an R group that varies between amino acids. ‘A peptide bond isthe bond formed by condensation reactions between amine acids. ‘A dipeptide is two amino acids joined by a peptide bond, A polypeptide is along chain of amino acis joined by peptide bonds. Fibrous proteinsare proteins that have long, parallel polypeptide chains with occasional eros linkages that form into fibres, but with ite erry steveture ‘Adisifde bonds strong covalent bond formed as a result ofan oxidation reaction between sufur troupsin opteine o methionine molecules which are close together in the suctue of polypeptide lobular proteins are ange proteins with complex tertiary and sometimes quatemary structures, folded into spherical (globular shapes Haemoglobin isa large conjugated protein involved in transporting oxygen in the blood, and gives the cerythnocytes their ted colour. Collagen is a strong fibrous protein witha triple helixstructure, Denaturation isthe loss ofthe 3D shape of a protein, eg. as. result of changes in temperature or pH. ‘A prosthetic group isthe molecule thats incorporated ina conjugated protein. ‘A glycoprotein sa protein with a carbohydrate prosthetic group, A protease is a protein-digesting enzyme. lipoprotein ca protein witha lipid prosthetic group. 31DRY EYES? etic TREHALOSE - A SUGAR FOR Biological molecules have an amazing number of different roles in living organisms, including some you ‘would not expect. In this activity you wil discover how current research, which shows that disaccharide tuchalose can protect proteins from damage in stressful conditions, is being used to make dry eyes more comfortable ~ and possibly protect the brain from the damage that can result from ageing. TREHALOSE: AN INTRIGUING DISACCHARIDE WITH POTENTIAL FOR MEDICAL APPLICATION IN OPHTHALMOLOGY Jacques Luyckx and Christophe Baudouin Abstract “Trohalose isa naturally occurring disaccharide comprised of two molecules of glucose. The sugar is widespread in many species of plans and animals, where is function appears to be to protect ells ‘aginst desiceaion, but it 8 not found in maarnmals. Treulose as the ability to protec cellular membranes and labile proteins against ‘damage and denaturation as a result of desiceation and oxidative tess. “Trehalose appears to be the most effective sugar for protection against ‘desiccation. Although the exact mechanism by which trehalose protects Jabile macromolecules and lipid membranes is unknown, credible ‘hypotheses do exist, As well as being used in lage quantities inthe ‘ood industry, trehalose is used inthe biopharmaccutical preservation ‘of labile protein drugs and inthe eryepreservation of hurnan cell, ‘Trehalose is under investigation for a number of medical applications, including the weatment of Huntington's chorea and Alzaeimer's disease. Recent studies have shown that trehalose can also prevent, ‘damage to mammalian eyes caused by desiccation andl oxida ‘insult. These unique properties of twhalose have thus prompted its ‘investigation as a component in treatment for dey eye syndrome. This interesting and unique disacchatide appears to have properties which ‘may be exploited in ophthalmology and other disease states. ‘Trehalose,a naturally occurring alpha-linked disaccharide formed ‘ortvo molecules of glucose (fig A)... is synthesized by many living organisms, including insects, plants, fungi, and micro- ‘omganisms as a response to prolonged periods of desiccation. ‘This very useful property, known as anhydrobiosis, confers on an ‘organism the ability to survive almost complete dehydration for ‘prolonged periods and subsequently reanimate, ‘Where else wil |encounter these themes? 32 HO OH ° ° Ho! 01 10H ud ‘OH HO ‘OH fig Strctuce of trehalose Regt number: 99-20-T: Mola ras 342236 gil annydrusl 37833 g/mol (hydrate) molecular Structure a D-glucopyranosy a D-glucopyranoside (aa ttehalos} References 1 Itusringa G, Susitez R, Nova-Franco B. Trehalose metabolism: From osmoprotection to signaling, Jnt J Mot Sei. 2009; 10:3793-3810, [..] 8 Elbein AD, Pan YT, Pastuszak I, Carroll D. New insights on tuehalose: A multifunctional molecule. Glycobiology. 2003; 1317R-27R. Jain NK, Roy 1. Eifect of trehalose on protein structure Protein Sci. 2009, 18:24-36. Matsuo T. Trehalose protects comeal epithelial cells from death by drying. Br J Oplihalmet. 2001; 85:610-612. [...] Matsuo T, Tsuchida Y, Morimoto N. Trehalose eye drops in the treatment of dry eye syndrome. Ophthalmology. 2002: 109:2024-2029. Matsuo T. Trehalose versus hyaluronan or cellulose in eyedops for the treatment of dry eye. Jpn J Oplulualmol. 2004; 48:321-327. 31CO eo Let us start by considering the nature of the writing in this article: 1. This extract comes from a paper published in Clinical Ophthalmology, an online journal Think about the type of writing being used and the audience itis intended for as you try and answer the following questions ‘a, What aspects ofthis writing tell you itis from a scientific paper rather than a general interest article in a magazine? bb. Choose two words used In the article that you are not familar with. Find out what [RURrnrwenrnnseny they mean and suggest why they have been used by the author of the article. Think about the tevay of | . How do you think these ideas about trehalose and the way it may be used to help Scientific detail that ig human health might be presented in a newspaper or on the BBC website? Have ago at ied for your expected | writing an article fora public interest website yourself Sidlence How wil yop 4. trehalose can really help protect people's sight and prevent brain diseases suchas || conc) ) 0" eile Huntington’s and Alzheimer’s this would make a big difference to people'slives. Notice |} 7” how cautious the author is. Wy are scientific papers so measured in the way they report - things? interesting Now you are going to think about the science in the article. You will be surprised how much you know already; but if you choose to do so, you can rerurn to these questions later in your course 4, Scientists think that trehalose protects both lipid membranes and certain proteins from learried les YOu have | Ineady and use it damage, both from drying out and oxidation. Explain why it isso important biologically [ect dae 2, What do you know about the chemical nature of trehalose from the article? Poosy, 3. Desiccetion (drying out) is a major problem for living organisms, Suggest reasons why (Rie ee drying out is so hard to survive. Lf | Bia shou the chemistry of ‘and how / OF this paper tof ences listed at the end. to online encyclopedias, to other \ ssientie papers ana ta Deoks In cach case juage | the reiabilty of to protect cell membranes and protein structures. \ trehalose works the refer fig Selaginelalepeophylaie a resurecton plant it can withstand almost complete dehyctatio ‘thin about 24 how, thane 0 high lev of trehalose in the pant cll, Which aspect of trehalose would you lke to know more about? The way it prevents desiccation in many groups of organisms? The way itcan protect human eyes from damage? The evidence that it could help reduce brain diseases in people? CChooke the area that interests you most and use as many resources as you can to produce a 3-minute presentation about that aspect of trehalose biology Find interesting images and lis all the references to help your colleagues decide if they can rely on the information you present (© From the flowing joel ace “Trehaose: an intriguing d-accharide wth poem for mca pplication in ophthalmolog Clinical Ophthalology (Gvukland.NZ) GOI) S771 Which statement best describes the structure or roe of these biological molecules? () Dissacharides can be split by ‘A. hydrolysis of glycosidic bonds B condensation af glycosidic bonds hydrolysis of ester bonds D_ condensation of ester bonds a (0) Amylose is an example of A. monosaccharide B disaccharide polysaccharide D tuisaccharide a (c) The role of starch isto A. be a souree of energy to plants B. store energy in all living orgenisms store energy in plants D. store energy in animals a (a) Proteins are polymers of amino acids joined by peptide ‘bonds formed between the ‘A. Rgroups B_ R group and the amino group © R group and the carboxyl group carboxyl group and the amino group a (e} The three-dimensional structure of a protein is held together by ‘A. peptide, hydrogen and ionic bonds B hydrogen, ester and ionie bonds disulfide bridges and ester bonds D. cisulfde bridges. hydrogen and ionic bonds a {°) DIVA consists of mononucleotides joined togther by bonds i ‘two pentose sugars cone ribose sugar and one phosphate group cone decxyribose sugar and one phosphate group ‘two phosphate groups a) goo Exam-style questions (a) Water is described asa polar molecule because it has @ A. positively charged hydrogen end and a negatively changed oxygen end B. positively changed hydrogen end and a positively ‘changed oxygen end negatively charged hydrogen end and a negatively changed exygen end D negatively charged hydrogen end and a positively charged oxygen end u) 2 Fill n this table to show the components and bonding within, each carbohydrate, ‘Component monosaccharides Bonds between ‘monosaccharides 3] [Total: 3] 3. A disaccharide can be hydrolysed to its two monosaccharides. Explain the tert hydrolysis. (2) [Total: 2] 4 Read through the following account on lipids, then write on the dotted lines the most appropriate words to complete the account. Lipids are insoluble in water because they are ‘Atriglyceride is one type of lipid. A triglyceride consists of ONE eee ‘molecule with three molecules joined to it by ‘bonds. Triglycerides have important roles in living organisms, including waterproofing ANG ee (5) (Total: 5)5 (a) Draw a diagram to show the structure of a phospholipid Use the symbols shown far each component in your ‘wen Ester bond: — 3] Glycerol Fatty acid: ———— {) The presence of a phosphate makes part of the molecule hhydrophilic. Explain what is meant by the term hydrophilic. {¢) Describe the role of phospholipids in the cell surface a (plasma) membrane. fe (Total: 6] 6 (a) Draw a triglyceride. You may use any component more than once. alycerol WAAAY Tatty acid ester bond {b) There are four statements about tialy If the statement is coreect, puta tick vighe of that statement. Ifthe statements incorrect, put 8 cross (fd) inthe box tothe right of the statement. Statement or eross (5) “Triglycerides are bulding blocks of polysaccharides “Tiilvcerides can contain a small armaunt of nitrogen “Triglycerides can be ‘modified into phospholipids “Triglycerides release water during hydrolysis (4 {) Fatty acids ean be either saturated or unsaturated, Explain Oy (Total: 5] ‘what is meant by the term saturated fatty acid 7 Describe the structure of an amino acid (2) (Total: 2} 8 (a) Insulin and collagen are both proteins thar have a primary structure made up of amino acids joined together by peptide bonds, () Explain what is meant by the term primary structure of a protein. a (i) Name the type of reaction that occurs when a peptide bond is broken causing a dipeptide to split into wo amino acids, () Insulin and collagen both contain the amino acids glycine and serine. The diagram below shows a dipeptide formed from these two amino acids. Complete the diagram to show the structure of serine when the peptide bond breaks. H. oO a Soe nel | 4 do bu moo i” netic + H ‘ ‘OH Giyene serine a (Total: 3]TOPIC 1 Biological molecules 1 8) Birelfeyeirer- mite) (yal ey Introduction In an air-conditioned room near Cambridge, ranks of machines at the Wellcome Trust Sanger Institute Sequence the genetic material of thousands of anonymous people, of disease-causing bacteria and of cancers ‘that mutate and grow in spite of chematherapy. Without noise, without drama, the secrets of life itself are revealed in bars of light as the ever-developing technology identifies the sequences of bases that make up the DNA code. The first complete sequence ofthe human genome tock yeas of work by scientists in many countries. Now ittakes days to complete a human genome and less than 24 hours to sequence the genetic ‘material ofa bacterium. The expertise of scientists is tll needed to interpret and use the information, which is being produced 24 hours a day. The potential benefits from ths rapidly developing area of science, where biology, medicine and computers come together, are almost limitless. In this chapter you willbe studying the nucleotides and some of the molecules in which they play a key role including DNA. ‘Adenosine tiphosphate (ATP) i the molecule that actsas the universal energy supply in cells of every type. You will ookat the structure ofthe molecule and how this is related to its ale in cells, You willbe reersing to ATP in almost every aspect of your biology studies. Nucleic acids or polynucleotides are the information molecules of the cel. You will discover the structure of deoxyribonucleic acid (DNA) and crack the code by which it carries the information needed to bulld an entice new organism. ‘You will earn about the different types of ribonucleic acid (RNA) and how they work together with the DNA, to translate the genetic code into the phenotype ofthe cell or organism through protein synthesis You also vill bull upa model of mutation and see how changes in the genetic code itself ean result in changes, which ‘may benefit or damage an organism, All the maths you need + Reet nise and make use of appropriate units in calculations (eg. nanometres) + Use ratios (9 representing the relationships between atoms in an ion or molecule)AE Mail ce Rll te See eee eee Poets DNA is the genetic material of the cel See Ree ae ete ecm pe ee eee ee eee SRE aM ep mre cae coed p ee et eer ce Cee ee a eeeree nt Dee ees ‘mutations and how they can affect the pher cee ait aaa (Alevel) Seen P Roem eal TOs Ee a ‘OF negative in thei effect eee Cellular respiration isan exothermic reaction that (Alevel) pee + Gene technology (A level) arc aU Rated Be eee connie Sen eens eevee] ern ee ee earl eee eee eer Reet Lan yaNucleotides and ATP By the end of this section, you should be able to.. © outline the structure of nucleotides, both purines and pyrimidines (© relate the structure and properties of ATP to its function in the cell Nucleotides Nucleotides are key molecules in biology: They provide the energy currency of cells in the form of adenosine triphosphate, usually reierred to as ATP. They also provide the building blocks for the mechanism of inheritance in the form of DNA - deoxyribonucleic acid ~ and RNA ~ ribonucleic Each nucleotide has three parts ~ @ 5-carbon pentose sugar, a nitrogen-containing base and a phosphate group. The pentose sugar in RNA is ribose, and in DNA is deoxyribose. Deoxyribose, asits name suggests, contains one fewer oxygen atom than ribose (see fig A) The most common types of nucleotides have either a purine base, which nar so rtogen containing ngs ora pyrimidine base which has only one. Both purines and pyrimidines are weak bases. The most common purines are adenine (A) and guanine (G)and the most eommon pyrimidines are eytosine(C), thymine (7) end uracil (1) A phosphate group (-PO,*) isthe third component of a nucleotide. [norganie phosphate ions ae present in the cytoplasm of every cell (see Seetion 1.1.1 for more about inorganic ions), It is as @ result of this phosphate group thatthe nucleotides are acidic molecules and carry a negative charge. The sugar, the base and the phosphate group are joined together bby condensation reactions, with the elimination of two water molecules, to form a nucleotide (see fig A). CHOH OH | nO) phosphate LSI — noooH/ Ny | | Note: DNA and RNA t—<¢ contain both phosphate and nitrogen (in the base). nH \ he ribose h, re ofa nucleo fig A The sc de. The propeies ofthe nucleotide 38 ATP. (Calls are chemical factories, with many reactions continually taking place within the cytoplasm and organelles (see Sections 2.1.3, ‘and 2.1.8 on cell structures and Book 2 Chapter 5.1 on cellular respiration), In these reactions, chemical bonds are constantly being broken and energy is always needed to break the bonds. Each cell needs a constantly available and immediately accessible supply of energy to support a multitude of different reactions. ‘One molecule seems to be the universal energy supplier in cells adenosine triphosphate (ATP). ATP is found inal living organisms in exactly the same form. Anything which interferes with the production or breakdown of ATP is fatal to the cell and ultimately estroys the whole multicellular organism, ATP is a nucleotide with three phosphate groups attached (ee fig B), [tis the potential energy in the phosphate bonds, that is nade available to cells for use in breaking bonds in chemical reaction: Fig B shows the structure of ATP When energy is needed in the cell, the third phosphate bond in the molecule is broken in a hydrolysis reaction, This is catalysed by the enzyme ATPase. The products of the reaction are adenosine diphosphate (ADP), ‘another nucleotide, and a free inorganic phosphate group (P), One phosphate bonds broken as the ATP is split ~ this uses energy Two further bonds are made to produce the ADP and the st phosphate group and ths releases the energy that is needed to drive cother reactions, About 34k! of energy are released per mole of ATP hydrolysed. Some of this energy is always lost to the system as heat, but the testis used for any enengy-requiring biological activity in the cell such as building up new molecules, active ransport (see Section 4.1.4), nerve impulses or muscle contraction. ior, of LN ey ee t__¢ LI OH OH deaxyribose ‘cuca tothe roles of ATP DNA and RNA©) DOO fig The struct of ATP The breakdown of ATP into ADP is @ reversible reaction, ATP can be synthesised from ADP and a phosphate group in a reaction tha requires an input of energy (30.51 per mole of ATP produced) ATPase catalyses this reaction, The direction of the reaction depends on conditions in the cel, The energy needed to drive the synthesis of ATP usually comes from breakdown reactions or ‘rom reduction /oxidation (redox) reactions. As a result. the ATP molecule provides an immediate supply of energy. ready for use when needed ‘coupled to catabolism, ‘eg respiration Sp (hd gi om 3 = hydrolysis energy coupled to anabolisn fig € The energy celeasodin catabolic reactions dives When need this energy can then Be used 0 inthe ca Cyanide and ATP Cyanide isa well-known poison that smell of bitter almonds. tis fatal because the poison blocks part ofthe process of cellular respiration producing ATP. Without ATP the ces ofthe body stop working. The muscles go into spasm and the victim cannot breathe, which rapidly results in death, ‘| Describe the structure of a nucleotide. 2. ArPis regarded as the universal energy supply molecule, Why is tis and how des its stucture relate to its role in cells? Key definitions [Nucleotides are molecules with three parts ~ a 5-carbon pentose sugar, a nitrogen-containing base and a phosphate group - joined by condensation reactions ‘Adenosine triphosphate (ATP) isa nucleotide that acts as the Universal energy supply molecule in call. It is made up of the base adenine, the pentose sugar ribose and three phosphate groups purine base isa base found in nucleotides that has two nitrogen- containing rings. [pyrimidine base isa base found in nucleotides that has one nitrogen-containing ring ‘Adenine isa purine base found in DNA and RNA, Guanine isa purine base found in DNAand RNA, CCytosine is pyrimidine base found in DNAand RNA ‘Thymine sa pyrimidine base found in DNA. Uracil is 2 pyrimidine base found in RNA ‘ATPase isan enzyme that catalyses the formation and the breakdown of ATP, depending on conditions. ‘Adenosine diphosphate (ADP) isa nucleotide formed when ATP loses a phosphate group and provides energy to drive reactions in the cell Reduction/oxidation (redox) reactions are reactions in which one reactant loses electrons (is oxidised) and another gains electrons (isteduced), 39)Nucleic acids By the end of this section, you should be able to.. © describe the structure of DNA including the structure of the nucleotides, base pairing, the two sugar-phosphate backbones, phosphodiester bonds and hydrogen bonds © describe the structure of RNA including nucleotides, the ssugar~phosphate backbones and the role of hydrogen bonds Reproduction is one of seven key processes in living organisms Ifthe individuals in a species do not reproduce, then that species will de out, Multicelular organisms also need to grow, and to replace worn-out cells. Within every cellis a set of instructions for the assembling of new cells. These can be used both to form offspring andi to produce identical cells for growth, (ver the last 75 years or so scientists have made enormous strides towards understanding the form of these instructions the genetic code. In unravelling the secrets of the genetic code, [people have come closer than ever before to understanding the mystery of life itself Nucleic acids, also known as polynucleotides, ae the information molecules ofthe cell. They are polymers, made of many nucleotide monomer units. They carry all the information needed to form new cells. The information fakes the form of a code in the molecules of DNA — deoxyribonucleic acid (see fig C) Parts of the code are copied into messenger RNA (mRNA) and used to direct the production of the proteins that build the cell and contro its actions. In eukaryotic cells, the genetic information is stored in chromosomes in the nucleus (see Section 2.1.3), but in prokaryotes a single length of DNA is found floating freely in the cytoplestn (see Section 2.2.1) Building the polynucleotides Nucleic acids are chains of muceoties inked together by condensation reactions that produce phosphodiester bonds between the suger on one muceotce andthe phosphate group of the next nucleotide These nace acids canbe mons of muceotde units long Both DNA and RNA have this sugar ploxphate backbone. Because the sugar of one nucleotide bonds tothe phosptate group af the nest naceotie, polymuceotides aay have a hyo group at one end and a phosphate group atthe other This structural feature i important inthe ole of the Trcic aid in the cll. Long chain of nudeotdes containing thebases CGA and T join together o form DNA, Chains of muceotdes contitng C.G. Aand U make RNA. Knowledge Of how these units jin togethee and the thre-cimensional 3D) structures in DNA in particulars the bass of our understanding of molecular genetics. 40 phosphate — cone nucleotide phosphate sugar and phosphate — join here by a phosphodiester bond formed by condensation sugar-phosphate | backbone | polynucleotide chain ‘bases stick out {gd polyruclocride stand ke this makes up the bas RNA molecules form single polynucleotide strands that can fold into complex shapes, held in place by hydrogen bonds, or remain as long thread-like molecules. DNA molecules consist of two polynucleotide strands twisted around each other. The sugars and phosphates form the backbone of the molecule and, pointing inwards from the two sugar-phosphate backbones, are the bases, ‘hich pair up in specific ways. A purine base always pairs with pyrimidine base —in DNA, adenine pairs with thymine and ‘cytosine with guanine. This results in the famous DNA double helix, a massive molecule that resembles a spiral staircase, se double he snicture af 2 DNA male ne cle of DNA The two strands of the DNA double helix are held together by hydrogen bonds betwen the complementary base pairs (see fig C). These hydrogen bonds form between the amino and the carbonyl groups of the purine and pyrimidine bases on the ‘opposite strands. There are three hydrogen bonds between C and Gout only two between A and'T: There are 10 base pairs for each ‘complete twist of the helix. The two strands are known as the §" (6 prime) and 3' (3 prime) strand, named according to the number cf the carbon atoms in the pentose sugar to which the phosphate ‘group is attached in the first nucleotide of the chain. [tis thephosphate that is free at the 5' end of the 5* carbon, and itis the free -OH group that is attached to the 3° carbon on the 3" end, ‘As you wil see, these features of the structure of DNA and RNA. are crucial to the way the molecules function within cells © tnydrogen bonds end i end Note the bases bre arranged in a specie sequence, sugar phosphate— backbone of one phosphate BNA Stand “deoxyribose ‘gut 2 ent \ “Send organic base (guanine) vn sugar pxphawe Purines Pyrimidines Patan bh N. ps ta mee Gre complete 1 ‘urn equals Ko 10 base pairs, Ww nid oF eH guanine cytosine he two strands are antiparallel ~ ne runs in one direction and the other in the apposite direction. eof ee pe depends on the hy [Make sue you use the terms nucleotide and nucleic acid correctiy = do not muddle them up. Did you know? Sequencing the genome From the late twentieth century onwards scientists from around the World collaborated inthe Human Genome Project. This was an ambitious project that set out to identify ll ofthe genes in the human chromosomes and to sequence the 3 billion base pairs which ‘make up the human DNA. The scientists worked on DNA from ‘anonymous danors and showed that every individual has at least 99.9% oftheir DNA in common. Leaps in technology meant the project finished ahead of the expected date, but stil took almost 13 years |n2008 a new project began - the 1000 Genomes Project. This time, scientists analysed the DN‘ of 1092 people from all around the world, to gain information about cferences in our DNA that can ‘amongst many things, have an impact on the diseases that may affect us. The 1000 Genomes Project took & years. The 10K (ten thousand) Genomes Project got under way in 2013, “This projects sequencing the genomes of 10000 people from around the world with rare genetic diseases and cancers. The whole 10K Genomes Project is expected fo take only 3 years, thanks to the immense improvements in sequencing technology, which mean that processes that once taok weeks and months now take hours and days Itshould greatly increase our understanding diagnosis and leven treatment of rare genetic conditions. ‘| What isa nucleotide monomer unit and which constituent parts are found in both DNA and RNA? 2 () tapan how complementary base paiing and hydrogen nang ae responsible or thes curef DNA (0) Lookcarfuly at te structural ormula ofthe purine bases toa the pine bases of te DNA molecule Suggest eens try thepars oft aos involve one pure ant one pidinebase, never purines or Wo priidnes, Key definitions [Nuclefe acids are polymers made up of many nucleotide monomer Units that cary all the information needed to form new cel ‘phosphodiester bond isthe bond formed between the phosphate igroup of one nucleotide and the sugar ofthe next nucleotide in a condensation reaction. [genome isthe entire genetic material of an organism aHow DNA works By the end of this section, you should be able to.. © explain how DNA replicates semiconservatively including the role of DNA helicase, polymerase and ligase ‘relate the structure of the DNA molecule to the way in which it replicates (One of the most important features of the DNA molecule is that it can replicate, or copy itsel, exactly. This is the characteristic above all others, that means it can pass on genetic information from one cell or generation to another Uncovering the mechanism of replication ‘After Watson and Crick had produced their double helix model for the structure of DIVA, it took scientists some years to work out exactly how the molecule replicates itself “There were two main ideas about how replication happens: conservative and semiconservative replication. In the conservative replication model, the original double helix remained intact and in some way instructed the formation of a new, identical double helix, made up entirely of new material, ‘The serniconservative replication model assumed that the DNA ‘unzipped’ and new nucleotides aligned along each strand, Each new double helix contained one strand of the origina DNA and one strand made up of new material. This was the ‘Watson and Crick hypothesis - the double helix would unzip along the hydrogen bonds in their structural model, allowing ‘semiconsevative replication to take place. It took classic piece of practical investigation to settle the argument Experimental evidence As the result of a very elegant set of experiments caried cut by Matthew Mese'son (1920-) and Franklin Stahl (1929-) at the California Insitute of Technology inthe late 1950s, semiconservative replication became the accepted model of DNA replication. + They grew several generations of the gut bacteria Escherichia coli(E: col) in a medium where their only source of nitrogen was the isotope "N from “NH,CL Atoms of N are denser than those of the isotope usually found, "N, The bacteria _grown on this medium took up the isotope to make the cell chemicals, including proteins and DNA. After several _generations, she entire bacterial DNA was labelled with "N (‘heavy nitrogen). + They moved the bacteria to a medium containing normal “NH Clas their only nitragen source, and measured the density of their DNA as they reproduced. a2 + Meselson and Stahl predicted that if DNA reproduced by conservative replication, some of the DNA would have the density expected if it contained nothing but "N (the original strands), and some of it would have the density expected if it contained nothing but !N (the new strands). However if DNA reproduced by semiconservative replication, then all of the DNA would have the same density, half-way between that of| ®Ne and "N-containing DNA. + They found that all DNA had the same density, half-way ‘between that of #N- and !*N-containing DNA and so DNA ‘must replicate semiconservatively Conservative replication, where the double helix remaing intact and new strands form on the outside, would give: § heavy DNA g 3 Replicates in medium, ‘eantaining only ight nitrogen ‘ight ON Half of the DNA molecules have 2 light strands and hall have 2heavy stands. heavy DNA ‘Semiconservative replication, where the double helix unzips and ‘each strand replicates to produce a second, new strand, would give: light DNA “Tight DNA replicate one, Sample 1 I inmedium ee ‘containing heavy DNA heavy DNA. 22 oy tex ‘i replicate All of the DNA has one heavy strand wae EIN and one light strand (ay) mee BBB somes generation “Tight hybrid Half of the DNA motecules have light DNA and half are hybrid with ‘one light and one heavy strand. fig The reuts of thexe experiments by Meseson and tah puta end to the theory of coneenatve replication of NAHow DNA makes copies of itself A careful look at the process of the semiconservative replication of DNA shows clearly the importance Of the structure and properties of the DNA molecule to its role asthe genetic material of the cell : || Makea flow diagram to descrite the replication of DNA. When the DNA replicates, the two strands of the DNA molecule ‘unzip’ along the line of hydrogen bonds and unravel This is brought about by the enzyme DNA. helicase. The strands act as| templates for the new DNA sands The double helix The exposed bases attract free DNA / nucleotides and new hydrogen bonds are formed between ‘matching base pairs. up and catalyses the of DNA, automatically coi up into the double helix as weak hydrogen bo ‘The result is two new strands of DNA identical with the original piece. The new molecules form within the structure. 2. How did the work of Meselson and Stahl destroy support for the model ofthe conservative replication of DNA? Key definitions \When @ ONA molecule replicates, it copies sof exactly DNA helicase isan enzyme involved in DNA replication that nips the two stands ofthe DNA molecule DNA polymerase isan enzyme involed in DNA replication that ines up and catalyses the linking up of the nucleoties ang the template strand DNA ligase is an enzyme involved in DNA replication that catalyses the formation of phosphodiester bonds between the two stands of DNA, DNA polymerase ines, ‘The chains of linking up of the nucleotides fit nucleotides along the teeth eve nplate strand. DNA as long as cytosine ligase catalyses the and guanine adenine formation of and thymine ar phosphodiester bonds = between the two strands Learning tip __ Make sure you are clear about the difference between conservative and semiconservative models of DNA replication and ean ‘explain how the evidence supports the second model BThe genetic code By the end of this section, you should be able to.. © define a gene asa sequence of bases on a DNA molecule coding for a sequence of amino acids ina polypeptide chain © explain the nature of the genetic code including triplets, codons, the degenerate and non-overlapping nature of the code and that notall of the genome codes for proteins We know that DNA has a double helix structure and ean replicate itself exactly. But how does DNA fact as the genetic material and carry the information needed to make new cells and whole new ‘organisms? The key isthe link between DNA and proteins, DNA controls protein synthesis and so the DNA instructions control not only how the cell is built, but also how it works. Proteins are made up of amino acids. Using the DINA code, the 20 naturally occurring amino acids ere joined together in countless combinations to make an almost infinite variety of proteins. This process Of translation hiappens on the surface of the ribosomes (see Section 1.3.5 on protein syntiesis) What is the genetic code? Inthe DNA double hel, the components that vary are he bases So scientists guessed that it was the arengerent of the bases tht caries the genetic code ~ but how? There are only four bases, 50 if one base coded for one amino aid there could be ony four amino aids. Even two bases do not igre enough amino acids the posible arrangement of four bases ito groups of two is 4% 4~ 16 However, a triplet code of three bases gives 4 x 4 x 4 = 64 possible combinations — more than enough forthe 20 amino acids that are coded fr Cracking the code The genetic code is based on genes. We can define a gene asa sequence of bases ona DNA molecule coding for sequence of amino aces in a polypeptide chain, tat affect e characteristic inthe phenotype of te organism. By the eat 19605 it had been proved tha a tiplt code of bases vwas the comerstone ofthe genetic code. Each sequence of tee bases along a strand of DNA Codes for something very speci Most code fra particular amino aid, but some triplet signal the Beginning or the end of one particular amino aid sequence ‘A sequence of three bases on the DNA or RNA is known as @ codon. The codons of the DNA are dificult to work out because the molecule isso large, so most of the work was done on the codons of the smaller molecule mRNA, ‘This mRNA is formed as a complementary strand to thie DNA, so i is lke a reverse image of the original base sequence. Once we know the RNA sequence, we can work ‘out the DNA sequence because of the way bases always pair:T/U with A, and G with C. Sequencing tasks lke this have become much easier in the twenty-first century as technology has advanced. The result of all this work isa sort of dictionary of the genetic code (see tables A and B). Much Of the original work, done in the 1960s, used the gut bacteria Ecol, but all the studies done since suggest that the genetic cade is identical throughout the living world Large parts of the DNA do net code for proteins, Scientists think the non-coding DNA sequences are ‘very important ~ 98% of the human DNA is non-coding, They know they are involved in regulating the protein-coding sequences - effectively turning genes on or off Many organisms have similar non-coding sequences, which suggests they are useful, ut in many cases we stil do nat know exactly what they do Im the 29 of the human DNA that codes for proteins, some codons code fora particular amino ac, while others code for the beginning or the ending of @ particular amino acid sequence. We now know that the genetic code is not only e triplet code, it is non-overlapping and degenerate as well, a4Did you know? DNA code-breakers ‘The ist brealahrough in decoding the genetic cede came in 1961 when MAW. Nicenberg (1927-2010) ane JH. Matthaei (1929-) in the Unite States prepared artificial mRNA where all the bases were uracil, They added their polyU ~ chains reading UUUUUUJUUUUU.- to all the other ingredients needed for protein synthesis (ribosomes, ‘RNAS, amino acids, ete). When they analysed the polypeptides made, they found chains of 2 single type of amino acid, phenylalanine. UUU appeared to be the mRNA codon for phenylalanine. So the DNA cadon would be AAA. The scientists soon showed that CCC cades for proline and AMA for lysine. Evidence for the triplet code - three non-overlapping bases with some degeneracy ~ built up swiftly feom this early work twas also shown that the minimum length of aificial mRNA that would bind toa ribasome was three bases long - a single codon, This would then bind with the Corresponding tRNA. From this point on it was a case of careful and precise work to identily all of the codons and their corresponding amino acids. second letter of the codon ee janine ATA “tyrosine cysteine - ‘aac Phen Fa aa arc - a as Miss im of, 3 jOAA, STA histidine Ag ER cs, cic : 6 & iB Gre, sane c& 5 TAA TTA | asparagine TEA serine ag BD tac sear Te Sp Teo og 2 Tar iran TIT TT ¥ ‘ mation Tr sine TCE inne 8 8 = CAA CTA geese ac cca -_" (CAD i ‘alanine ro COS gycine - Sod CTT glutamic acid val 7 cac crc | ccc . a ee phenylalanine ven UAL tyrosine UCU cystine u OUR eure veA BR stop codon TaD topes a 3 uu cou ‘CAU cou U rs i ae con coe ea ad cus COG) A glutamine ‘cos o§ BPN i iinene AS henin eg 3 oe feel yin a8 3 cones: ace cs og = Baw GAL gape acid cou: my cut ICC Gac. occ c - = = uA if GAA shure seid ewe A ineallwcekon genetics the RNA eo table 8 The ips cod tatu 4546 Anon-overlapping code... ‘Once scientists had worked out that the genetic code was based on triplets of DNA bases, they wanted to find out how the code was read. Do the triplets of bases follow each other along the DNA strand like beads on a necklace, or do they overlap? For example, the mRNA sequence UUUAGC could code for two amino acids, phenylalanine (UUU) and serine (AGC). On the other hand, if the code overlaps, it could code for four: phenylalanine (UUU), leucine (UA), a nonsense or stop codon (UAG) and serine (AGC) An overlapping code would be very economical ~ relatively short lengths of DNA could carry the ictions for many different proteins. However it would also be very limiting, because the amino acids that could be coded for side by side would be limited. In the example given, only leucine out Of the 20 available amino acids could ever follow phenylalanine, because only leucine has an mRNA codon starting with UU tists rely on experimental observations to help decide whether the genetic code is overlapping (or not. IF a codon consists of three nucleotides and is completely overlapping, and a single nucleotide is altered by a point mutation, then three amino acids will be affected by that single ‘change. If the code is only partly overlapping, shen a single point mutation would result in two affected amino acids. Buf the codons do not averlap at all, chen a change in a single nucleotide ‘mutation would affect only one amino acid, which is what has been observed, for example in sickle cell disease, All the evidence available suggests thatthe code is not overlapping and this is generally accepted among scientists and a degenerate code ‘The genetic code contains more inormation than is needed. you Took carfilyat tables A and B, you wil sce that often only he fist two of the three maleate ina codon soem fo matter in determining which amino aid Yeults This may seem a rater useless feature a frst. bu if each aminoacid was produced by onl ene codon then any error or mutation could cause have. With, a degenerate (or redundant) code, if the final base in the triplet is changed, this mutation could still produce the same amino acd and have no effect onthe organism. Only methionine and tryprophan Ee represented by only one codon, Mutations can happen any time the DNA is copied ~ the degenerate code at least partly protects living organisms from their effects. ‘1 Explain what is meant by the genetic code. 2. whatismon-coding ONA? 3. whatare the benefits to an organism of ving (0) anon-evestpping code? (b) a degenerate code? Key definitions “Translation isthe process by which proteins ate produced, via RNA, using the genetic cade found in the DNA It takes place on the ribosomes. Ribosomes are the ste of protein synthesis inthe cell. triplet code is the code of three bases, and isthe basis ofthe genetic information in the DNA. ‘A gene isa sequence of bases on a DNA molecule. It contains coding fora sequence of amino acids in a polypeptide chain that affect a characteristic in the phenotype ofthe organism, A codon is a sequence of three bases in DNA or mRNA. ‘A complementary strand isthe strand of RNA formed that complements the DNA acting asthe coding sand,DNA and protein synthesis By the end of this section, you should be able to... (© describe the structure of mRNA including nucleotides, the sugar-phosphate backbone and the role of hydrogen bonds © describe the structure of tRNA including nucleotides, the role ‘of hydrogen bonds and the anticodon © explain the processes of transcription in the nucleus and translation at the ribosome, including the role of sense and antisense DNA, mRNA, tRNA and the ribosomes In eukaryotes, the DNA that codes for the individual proteins Js in the nudes of the cell. The ribosomes where proteins are synthesised are in the cytoplasm, DNA from the nucleus has never been detected in the cytoplasm, so the message cannot be carried direetly. RNAs (ribonucleic acids) carry the information from the nuclear DNA to the ribosomes, Different types of RNA RNA is closely related to DNA (see Section 1.3.2). However, it contains a different sugar (ribose) and a different base (uracil instead of thymine). It consists of a single helix and does not form enormous and complex molecules ike DNA. The sequence of bases along a strand of RNA relates to the sequence of bases on ‘a small part of the DNA in the nucleus. RNA enables DNA to act ‘as the genetic material. It carvies out three main functions in the process of protein synthesis: + It carries the instructions for a polypeptide from the DNA in the nucleus to the ribosomes where proteins are made ‘+ Itpicks up specific amino acids from the protoplasm and cartes them to the surface of the ribosomes. + Iemakes up the bulk of the ribosomes themselves. To perform these three very different functions, there are three different types of RNA. Messenger RNA Messenger RNA (mRNA) is formed in the nucleus, Whereas a double helix of DNA carries information about a vast array of proteins, a piece of mRNA usually has instructions for one polypeptide, The messenger RNA forms on the template or antisense strand of the DNA. The mRNA formed codes for a polypeptide, The coding strand of DNA is known as the sense strand of DNA. Any mRNA formed on this strand would be nonsense and would not code for a protein. Parts of the DNA molecule unravel and are transcribed onto stran of mRNA by an enzyme called DNA-directed RNA polymerase, This enzyme is often known as RNA polymerase, but the full ‘name tes you it polymerises nucleotide unis to form RNA ina. sequence determined by the DNA, The complementary bases in the nucleotides of the DNA and RNA line up alongside each other RNA nucleotides from the nucleoplasm lne up alongside the exposed DNA. Initially hydrogen bonds hold the complementary RNA bases in place. Then DNA-directed RNA polymerase catalyses the formation of phosphodiester bonds between the sugars and phosphate groups of the bases, to form a strand of ‘mRNA, Hydrogen bonds maintain the helical structure of the RINA molecule. Just as in the DNA, the bases of the mRNA forrn a tplet code and each triplet of bases is @ codon. The relatively small mRNA molecules pass easily through the pores in the nuclear membrane, carrying the instructions from the genes in the nucle to the eytoplasm, They then move (othe surface of the rbasomes, ‘where protein synthesis takes place (see fig A) sense ~ antisense (coding) (template) strand strand Inside the nucleus a portion ofa DNA molecule ‘opens up by breaking hydrogen bonds to reveal the sequence of nucleotide bases. Free RNA nucleotides hydrogen-bond conto the exposed bases, following complementary base pairing rules so Unonds with A, A with T,C with G and G with C |maNA : \ Passes out ofthe nucleus \ nucleus } | into the cytoplasm. Ie caries \ acopy ofthe instructions for \ | raking a protein 47Remember! mRNA smade on the antisense (template) strand ofthe IDNA, not the sense (coding) strand Transfer RNA ‘Transfer RNA (tRNA) is found in the cytoplasm. Ithas @ complex shape, often described as a clover leaf, that enables it to carry out ts function (see fig B). This shape iste result of hydrogen bonding between ciferent bases. One part of the tRNA molecule has a sequence of three bases that matches the genetic code of the DNA and corresponds to one particular amino aci. ‘This sequence of three bases is called the anticodon. Each ‘tRNA molecule also hes a binding site with which it picks up one particular amino acid from the vast numbers always fee in the eytoplasin “The RNA molecules, each carrying a specific amino acid, line up alongside the mRNA on the surface of the ribosome. ‘The anticodons of the tRNA line up withthe codons of ‘the mRNA. held in place by hydrogen bonds between the corresponding bases. Because the anticodon has a sequence of ‘bases that align withthe corresponding bases in the mRNA on the rbosornal surface, the carect sequence of amino acids is assembled. Once the amino acids are lined up together, peptide bonds form between them, building up a long chain of amino acids. I binding site wt forte =e ‘The anticodon - aminoacid = {S these three bases FEE deternine precisely to whieh piece of mRNA an the THINS) ribosomal surface As. the tRNA will join, ‘This in turn decides ‘clover leaf shepe J 3 the exact order of the q amino acids in the resulting polypeptide rm Wu uw chain fig There ae 61 types of NA molecules avallable to cary alle necessary amino aids (0 ce surface of the bosoms ready Fox eymessinio protein mavecules, 48 Ribosomal RNA Ribosomal RNA (FRNA) makes up about 50% of the structure cf a bosome and is the most common form of RNA found in cells It is made in the nucleus, under the control of the nucleoli and then moves out into the cytoplasm where it binds with proteins to form ribosomes. The ribosomes consist of a large and ‘small subunit. They surround and bind to the parts of the mRNA that are being actively translated, and then move along to the next codon, Their job is to hold together the mRNA and ¢RNA and act, as enzymes controlling the process of protein synthesis. Protein synthesis ‘To summarise, in the process of protein synthesis the genetic code of the DNA of the nucleus is transcribed onto messenger RNA. ‘This mRINA maxes out of the nucleus into the cytoplasm and becomes attached to a bosome. Molecules of transfer RNA camry individual amino acids to the surface of the ribosome. The tRNA anticodon lines up alongside & complementary codon inthe mRNA. held in place by hydrogen bonds while enzymes lnk the amino acids together ‘The tRNA then breaks away and returns o the cytoplasm to pickup another amino acid, The ribosome maves along the ‘molecule of mRNA unti i reaches the end, leaving a completed polypeptide chain. The message may be read again and again. Protein synthesis, like many other events in living things, is @ continual process, However, it makes it simpler to understand if ‘we look at the two main aspects of it separately ‘The events in the rnucleus involve the transcription of the DNA message (see fg A). In the cytoplasm that message is translated into polypeptide molecules and hence into proteins (see fig C). ‘Learning tip Be clear about the difference between transcription and translation. Mass production ‘The cytoplasm of cells contains many polysomes. ‘These are ‘groups of ribosomes joined by a thread of mRNA, and they appear to be a form of mass production of particular proteins, Instead of one ribosome moving steadily along a strand of mRNA. ‘and producing its polypeptide and then repeating the process, ribosomes attach in a steady stream to the mRNA and move along ‘one after the other producing lots of identical polypeptides. ‘This is how the genetic code carried on the DNA is translated into living material by the synthesis of proteins.1 TRANSCRIPTION DNAstrancs DNA information copied to mRNA sil joined template strand! DNA FieemRNA mucieotides SR DNA strands separate at one gene ‘mRNA stzand copied from template strand of DNA; {RNA detaches tocollee ancsher| ky amnoacid\ COG ee e growing polypeptide chain < peptide bond mRNA strand being assembled toatachamina pe ATP acid toRNA GOS gen (eaticedon) sino aid ee AUSGCEEAGAUGECCCAC —&Ee vncsome Tmoves long 5 snRNA realign codons Completed polypeptide modified ‘to produce functional protein, ‘eg enayime ofa specie shape codon of mRNA attracts ‘matching (RNA anticodon 4 ‘TRANSLATION mRNA information translated into a ‘specific sequence of amino acids tion loin the DN ‘1 DNAand RNAare the information molecules ofthe cell Explain the differences in the basic structures ofthese two molecules 2 tnmany organisms the DNAisin the naleusof the cls ad the prota foruhch code re nthe cnopism Span cretly the oes ofthe fllowinginandatng he genet code nto an ive enaymein the cjepasm of acl (@) DNA (©) messenger BNA (transfer RNA (@) ribosomal RNA ine rucleusis slated nto a Sequence of amino acidsin poly Key definitions ‘Messenger RNA (mRNA) isthe RNA formed inthe nucleus that caries the genetic code out into the cytoplasm. ‘The antisense strand {template strand) isthe DNA strand that codes for proteins. DNA cirected RNA polymerase (RNA polymerase) is the enzyme that polymerises nucleotice units to form RNA in a sequence determined by the antisense strand of ONA Transfer RNA (tRNA) molecules are small units of RNA that pick up Particular amino acids from the ooplasm and transport them tothe surface of the ribosome to align withthe mRNA “The anticodon isa sequence of three bases.on *RNA that are complementary to the bases in the mRNA codon. Ribosomal RNA (FRNA) is BNA that makes up about 50% of the structure of the rbosome Polysomes ae groups of ribosomes, joined by a thread of mRNA, that can produce large quantities oF a particular protein. “The sense strand of DNA has the same base sequence as the mRNA transcribed from the antisense strand, 49Gene mutation By the end of this section, you should be able to.. © explain the term gene mutation and describe base deletions, insertions and substitutions © explain the effect of point mutations on amino acid sequences as illustrated by sickle cell disease in humans ‘The genetic code carried on the DNA is translated into living cellular material through protein synthesis Ia single codon is changed or misread during the process, then the amino acid for ‘which it codes may be different. As a result the whole polypeptide chain and indeed the final protein may be altered, A change like this is known as a mutation. A mutation is a permanent change inthe DNA of an organism. A mutation can happen when the ‘gametes (00x cells) form, although they also oceur during the division of somatic (body) cells. Atiny alteration at this molecular level may have no noticeable effect at all but it may have devastating effects on the whole organism. Many human genetic diseases are the result of random mutations in ‘the generic material of the gametes. including thalassaemia, in which the blood proteins are not manufactured correctly, or eystc fibrosis, in which ¢ membrane protein does not function properly. Different types of mutations Gene mutations involve changes in the bases making up the codons. The chance of « mutation taking place during DNA replication is around 25 X 10% perbase, though estimates vary widely a itis very dificult to measure. Fortunately the body also has its own DNA repair systems. Specific enzymes cut out dr repair any parts of the DNA strands that become broken or damaged, In spite of this, some mutations remain and are copied fom the DNA when new prozeins are made Some mutations occur when just one or a small number of nucleotides are miscopied during transcription. These are point or gene mutations. If you think of the amino aci¢s| produced from each codon as the equivalent of the letters of the alphabet, the result of a point mutation is ike changing a letter in one word, It may well still make an acceptable word, but the ‘meaning wil probably be different, These gene mutations include substitutions, where one base substitutes for another deletions where a base is completely lost in the sequence, and insertions, when an extra base is added, which may be a repetition of one of the bases already there ora different base entirely Chromosomal mutations involve changes in the positions of ‘genes within the chromosomes. This is ike rearranging the words within a sentence — if you are lucky they stil make sense, but it will not mean the same as the original sentence. Finally there are ‘whole-chromosome mutations, where an entire chromasome is either lost during meiosis, which is cell division to form the sex cells, or duplicated in one cell by errors in the process, 50 ‘This is lke the loss or repetition of a whole sentence. For example, Down's syndrome is caused by a whole-chromosorne mutation at chromosome 21 ~ affected individuals have three copies of this, chromosome instead of the usual two. How gene mutations can affect the phenotype Mutations can be a source of variation within an organism, If the cifferent arrangements of nucleotides code for the same amino acid (see Section 1.3.5) a point mutation will have no effect. \Very occasionally, a mutation occurs that results in the production cf a new and superior protein. This may help the organism gain a reproductive advantage so that it leaves more offspring than ‘other individuals of that species, particularly if environmental conditions change. Most mutations are neutral, meaning that they neither improve nor worsen the chances of survival. Some ‘mutations cause great damage, disrupting the biochemistry of the entire orgenism. If a base mutation change isin a protein that plays an important role in a cell for example, the active ste of an enzyme ~ the elfect can be catastrophic. Sickle cell disease - when the code goes wrong Sickle cell disease is « genetic disease that affects the protein ‘chains making up the haemoglobin in the red blood cells. Its the result of a point mutation. A change of ane base in one codon ‘changes a single amino acid in a chain of 147 amino acids bout that change alters the nature of the protein, As a result, the haemoglobin molecules stick together to form rigid rods that give the red blood cells a sickle shape. They do not carry oxygen very efficiently and biock the smallest blood vessels ‘Tis single tiny ‘change in one nucleotide is enough to cause the people affected severe pain and even death, eae Pe ag [Gra | cac | ac de cell haemoglobin act | cc start | val | His | leu | Thr | Pro table A The cnange inte single coon tat causes ice cel esas (he re rine coders only shown)@ Function of protein DKA mRNA © Polypeptide chan polypeptide is 0 r ania neds fem aspeat A OU e é ‘ c 2 : i —- F fe ‘ Ri @ OMB Ros cs Sree L hcl ft @ DONA mBNA—_ CD Paipeptide Function o am ‘codons are ‘amino acid e slypeptide fol tgs srt oa me eet = fete conn assoc thebondto hold ea toa eooocccospe> eens rnsing ‘ing she dhcae ida femot bl © Polypeptide @ Furcions pet ~ ~onec ss 1 © at Eg Que. onebase |T A @: pe of active irs @ cut OM @@ figA Two cramples of how rence the phenoiype fig Thergidsh propery inthe boo ofthe redblood cells in sce cl cinease a a result of plain molecules prevents them rem unetoning Mutations can happen to any cell at any time, though they occur most commonly during the copying of DNA for cel division, Mutations in the body cells can cause problems such as cancer. The most damaging mutations occur in the gametes because they swillbe passed on to future offspring, These are the mutations that give rise to genetic diseases. Exposure to mutagens, as X-rays, jonising radiation and certain chemicals, increases the rate at which mutations occur For this reason itis better to keep exposure to these mutagens to a minimum. 1 Somebase mutations wl havea bigan impact onthe way the body works aay cvomosoral or whole ehvomosore mutton, Cine hee noe! sal onthe gana pa 2 euplam how change na single base nthe se cel nation has sucha damat eee onafestedinahdals A ‘A mutation i a permanent change in the DNA of an organism Gametes are haploid sex cells produced by meiosis that fuse to form ‘a new diploid cel (zygote) in sexual reproduction. [point mutation (gene mutation) isa change in one or a small number of nucleotides affecting a single gene ‘A substitution isa type of point mutation in which one base ina gene is substituted for another. [deletion is type of point mutation in which a base is completly lst. Aninsertion is atype of point mutation in which an extra base is added into a gene, which may be a repeat or a different base, Chromosomal mutations are changes inthe postion of entre genes within a chromosome Awhole-chromosome mutation is te oss or duplication of a whole ehramesome Sickle call disease (sickle cel anaemia) isa human genetic disease atfecting the protein chains making up the haemoglobin in the red biood calls /Armutagen is anything that increases the rate of mutation, 51ie) 1 (a) The diagram below shows the structure of a nucleotide ‘monomer unit from a DNA molecule. Name the parts labelled A and B. a) () The table below shows the percentage of different bases, present in the DNA from a cov. ‘Adenine [Guanine [ Thymine 2 Cytosine (Complete the table to show the percentage of adenine, guanine and cytosine in the DNA of the cow (1) (i) Explam how you worked out the percentage of guanine present inthe DNA of a cow 3) (Total 5} 2. The diagram below shows part of a DNA molecule. key ate _ pmimine hydrogen bond (a) Draw a ring around one nucleotide monomer unit. (1) (©) Name the two purine bases found in DNA, “ (c) (i) State where transcription takes place in eukaryotic cells, fe (i) During transcription, part of a DNA molecule unwinds and the DNA strands separate, Describe the events that follow to produce a messenger RNA (mRNA) molecule. 8) Exam-style questions (¢) Oligonucleotides are short chains of nucleotides. Some of these are man-made and have been used as drugs to treat awide variety of ciseases. They work by binding to mRNA. or DNA and inhibiting protein synthesis. The drugs are described as antisense drugs when they bind to mRNA and triplex drugs when they bind to DNA. (i) State which stage of protein synthesis willbe inhibited by each ofthe following + Antisense drugs + Triplex drugs a) (i) The table below shows the sequence of bases in part cf a molecule of mRNA. Complete the table to show the sequence of bases inthe antisense drug that will bind to this partof the mRNA molecule a (Total 8} 3 (a) Work by Nachman and Crowell (Gents, September 1, 2000 vol. 156 no, 297-304) using human DNA has estimated an average mutation rate of 2.5 x 10+ per base Assuming there are 7 10° base pai in a human diploid cell, calculate the average number of mutations formed each time the cell divides. e) (0) Ifa cell divides 50 times calculate the total number of mutations accumulated by an average cell u (c) Explain why most cells sill produce proteins that work properly despite this number of mutations. 6) (Total 6) 4 The diagram below shows some cell structures involved in protein synthesis in eukaryotic cells ‘Rough endoplasmic reticulum{@) Describe the events that occur inside the nucleus to produce a molecule of messenger RNA (mRNA). [4] {b) Describe the role of the bosomes in protein synthesis. [3] {c) The table below gives some of the base triplets on DNA that code for some amino acids and stop signals Base triplet on DNA | Amino acid/stop signal cee Glycine ‘AAA or AAG Phenylalanine ‘AGA or AGC Serine ecg ‘Arginine Tor Lysine ‘AT or ATC or ACT ‘Stop signal "The diagram below shows the final base triplets of a gene labelled T1 to TS, and the complementary messenger RNA (mRNA). ‘The sequence of amino acids atthe end of the protein produced is also shown, ToT 13 THT Last part of the DNAsmond [| CCC] ccc] acc] tr Complementary mRNA: Amino acid [aiyeine] Uf Lf sequence: : () Write in the codons found on the mRNA complementary to the base triplets T1, T2, 73, T4 on the diagram above. Q) (Using the information in the timetable, complete the amino acid sequence shown in the diagram above. ‘The first one has been done for you. @ (Gi)_Use the information in the table to deduce a base tiple for T5 on the DNA strand, ie [Total 12] 6 IDNA, the type of bond that joins deoxyribose sugar to a phosphate group is {@) aphosphodiester bond {b) alrydrogen bond (0) peptide bona {@) aglycosidic bond a [Total 1] 7 ‘The sequence CCGAAACGACTC on a DNA strand when transeribed would form which mRNA sequence? (@) cccuuuccUCAC (b) GGCUUUGCUGAG (c) CCGAAACGACUC (d) GGCAAAGCAGTG: 0) [Total 1] 8 The strand of DNA that is transcribed is called the (a) sense strand (b) antisense strand (c) same sense strand (d) missense strand ay (Total 1] © Meselson and Stahl's experiment showed that DNA replicated ‘semiconservatively. Bacteria grown on a medium containing ®N aver many generations would have DNA containing this ‘one isotope of nitrogen. ‘They were then transferred to grow on a medium that contained “IN, (@) Describe how these enzymes are used in DNA replication {) DNA helicase (2) (i) Polymerase 8) (i) Ligase a (b) Calculate the proportion of bacterial DNA that contains exclusively "Netter the third rund of replication. (2) (c) The strands of DNA were separated according to their density. Explain why it was necessary that '°N isa stable isotope of nitrogen. a () If DNA replicated conservatively then the results after the first round af replication would have differed fram the observed result with semiconservative replication Describe how the DNA strands formed by one round of semiconservative replication differ from those that might have formed from one round of conservative replication, (2) {Total 12]Enzymes Around the world, people have observed albino forms in almost every species of vertebrate, including human beings True albino animals are very striking - they have pure white hair, furor feathers, usually with pale skin and red or pale blue eyes. Albinism is genetic - itis inherited in the genes passed on from parents to ther offspring, But why do albino animals lack colour? Its all down to the lack ofa single enzyme - tyrosinase. This enzyme ia key factor inthe production ofthe pigment ‘melanin and other pigments) from the amino acid tyrosine. Diflering amounts of melanin, combined with other pigments, result ina wide range of har, skin and feather colours. If the enzyme is lacking, the animal lacks pigment and is albino, In this chapter you wil be looking at enzymes - their structure, how they work and what happens when they are inhibited. You B > williookat the varying roles of enzymes in the body and how they are named. Youwill go on to discover how enzymes work and how their mechanism of action is related to the shape ofthe active site produced within the tertiary structure of the protein itself. By looking atthe evidence you will see how our models of enzyme action have changed from the relatively simplistic lock and-key theory to the more complex induced-ft made! Measuring the rate of enzyme controlled reactions is key to understanding the factors thataffect them. You wil be considering the practical difficulties of doing this and how they can be overcome. Looking at the factors that affect the rate of an enzyme controlled reaction helps to build up our model of how enzymes act as catalysts in biological systems. Understanding how enzyme action can be inhibited by other molecules is another way of developing an understanding of hove enzymes work. You will conser competitive, non-competitive and ireversibe inhibition, 2s well as considering the situation ‘when the end products ofa long chain of reactions inhibit an enzyme earlier in the process Recognise and make use of appropriate units in calculations (eg. the units forthe ro of reaction of an enzyme) Use of percentages (9. calculating percentage yields in ciferent enzyme controlled reactions) Use of appropriate numberof significant figures (eg. understand that results for enz to the limits ofthe least accurate measurement) rate experiments can be reported or Find arithmetic means (eg, the mean ofa range of data when investigations are repeated) Plot range of data in an appropriate format (9. enzyme activity over time represented on a graph) Solve algebraic equations (eg. calculate the rate of enzyme reactor Plot two variables from experimental or other data investigations into enzyme controled reactions) Understand that y= mx + crepresents a linear celationship and predictor sketch the shape of a graph with a linear relationship (eg. the effect of substrate cancentration on the rate ofan enzyme controled reactian with excess enzyme) select an appropriate format for presenting data from experimental Calculate the rate of change from a graph showing a linear relationship (eg the rate of an enzyme contrlled reaction), Draw and use the slope ofa tangent toa curveasa measure of rate of change and use this method to measure the gradient ata point on a curve (eg. amount of product formed plotted against time when the concentration of enzyme i fixed) Mth xcee ercr Se eae cee ee HV Be STE aOR ep ares Se gece ean reactions inside and outside of cel The pos within cell organelles Beat Deen (level) eter eee ee) ity Warmer Mau Rute Tied rnin ener rnin The spe tive ste Se ea) peers See eer eee ees eee ae Bootes eee Srey See ee cee etree ead Doc teue tea id end-product inhibition - and See eer organism Ae il, SgBy the end of this section, you should be able to.. © describe the structure of enzymes as globular proteins © explain the concept of specificity © recognise that enzymes catalyse a wide range of intracellular reactions as well as extracellular What is an enzyme? A catalystiis a substance that changes the rate of a reaction without changing the substances produced. The catalyst is unaffected at the end of the reaction and can be used again, Enzymes are biological catalysts, which control the rate of the reactions that take place in individual cells and in whole organisms. Under the conditions of temperature and pH found in living cells, most of the reactions that provide cells with energy and produce new biological material would take place very slowly ~ too slowly for life to exist. Enzymes make life possible by speeding up the chemical reactions in cells without changing the conditions in the cytoplasrn, Enzymes are globular proteins (sce Section 1.2.4), produced during protein synthesis as the mRNA transcribed from the DNA molecule is translated (see Section 1.3.5). They have a very specific shape as a result of their primary secondary, tertiary and quaternary structures (see Section 1.2.4) and this means each enzyme will only catalyse a specific reaction or group of reactions. We say ‘enzymes show great specificity. Chianges in temperature and pH allect the elliciency of an enzyme ‘because they affect the intramolecular bonds within the protein that are responsible for the shape of the molecule. Within any cell many chemical reactions are going on at the same time. Those reactions that buile up new chemicals are known as anabolic reaetions (‘ana’ means up, as in ‘build up’). Those that break substances dawn are eatabolie reactions ‘cata’ means down), The combination of these two processes results in the complex array of biochemistry that we refer to as metabolism, Most of the reactions of metabolism occur not as single events but as part of a sequence of reactions known as ‘a metabolic chain or metabolic pathway. We usually think of enzymes speeding up reactions but sometimes they act to slow them dawn, or stop them completely fig A. Each coll contains sverl hundred diferent enzymes to contal the multitude cf reactions gong on inside 56Naming enzymes In the study of biology, in medicine, in cellular and genetic research and in industries that use biotechnology. its important tobe able to refer to the action of specific enzymes. To do this we need ta understand how enzymes are named, Many of the enzymes found in animals and plants work inside the cells These are known as intracellular enzymes, for example DNA polymerase and DNA ligase. Cells secrete other enzymes. that have an effect beyond the boundaries of the cell membrane ‘These are extracellular enzymes. The digestive enzymes and lysozyme, the enzyme in your tears, are well-known examples of these, Mest enzymes ~both intracellular and extracellular ~ have several names including «+a relatively shore recommended name, which is often the name ‘of the molecule that the enzyme works on (the substrate) with ase’ on the end, or the substrate with an indication of what it does, eg creatine kinase + longer systematic name describing the type of reaction being catalysed, e.g. ATPicreatine phosphotranslerase + a classification number, eg BC27.3.2 Some enzymes, such as urease, ribonuclease and lipase, are known by their recommended nares. But there a ‘enzymes that are kmown by common but uninformative names ~ trypsin and pepsin for example, However, the names of most ‘enzymes give you useful information about the role of the enzyme in the cell or the body. Didyouknow? The discovery of enzymes In 1835 people noticed that starch is broken down to sugars more effectively by malt (sprouting barley) than by sulfuric acid People also suspected there were Yerments in yeast la single-celled fungus) that turned sugar to alcohol and in 1877 the name enzyme (literally in yeast) was introduced. In 1897 Eduard Buchner (1860-1977) extracted a juice’ from yeast cells that would breakdown various sugars outside a living cell In 1926 James 8. Sumner (1887-1955) extracted the fst pure crystalline enzyme from jack beans. It was urease, the enzyme that catalyses the breakdown of urea. Sumner found the crystals were protein and concluded that enzymes must therefore be proteins Unfortunately no-one believed the young researcher at the time, because many established scientists had been trying and faling to isolate enzymes for years. However, 20 years later Sumner received a Nobel Prize for his ground-breaking work. igh Pure urease dees nat look very exciting, but the abityto sate ar ctract enaymes has revalutonized ou ‘waywe ease enzymes in sty ‘| From which organisms were the first enzymes isolated? derstanding of biology ana the 2 Whats the difference between an intracellular enzyme and an extracellular enzyme? 3 vestigate Sumner’ wrk and discover which scientists were ptr agatha and why Key definitions ‘catalyst sa substance that speeds up a reaction without changing the substances produced or being changed itself, Enzymes ae proteins that have a very specific shape as a result of their primary, secondary tertiary and quaternary structures. They act asbiological catalysts and each enzyme will only catalyse a specific reaction or group of reactions, Specificity isthe characteristic of enzymes that means that as a result ofthe very specific shapes resulting from their tertiary and {quaternary structures, each enzyme wil only catalyse a specific reaction or group of reactions ‘An anabolic reaction isthe reaction that builds up (synthesises) new ‘molecules ina cel ‘catabolic reaction isa reaction which breaks down substances within a cell ‘Metabolism isthe sum of the anabolic and catabolic processes in cell [Ametabolic chain (metabolic pathway) 2 series of inked reactions in the metabolism of a cell Intracellular enzymes are enzymes that catalyse reactions within the cell Extracellular enzymes are enzymes that catalyse reactions outside (ofthe callin which they were made 37How enzymes work By the end of this section, you should be able to. © explain how enzymes act as catalysts by reducing the activation energy of reactions © explain how the initial rate of enzyme activity can be measured and why thisis important © explain how different factors affect the rate of enzyme activity For a chemical reaction to take place, the reacting molecules must have enough energy to break the chemical bonds that hold them together A simple model is that the reaction has to get over an ‘energy hill’, known as the activation energy, before it can get started. Raising the temperature increases the rate of a chemical reaction by giving more molecules sufficient cenergy to react. However, living cells could not survive the temperatures needed to make many cellular reactions fast enough ~ and the energy demands to praduce the heat would be enormous. Enzymes solve the problem by lowering the activation energy needed for a reaction to take place (see ig A) x | activation e (uncatalysed) Q x activation energy B 5 catalyses) 8 | (reactants) z @ Final sate (products) Progress of reaction (ime) —> @= Energy of transition state in uncatalysed reaction @®= Energy of transition state, ie, enzyme/substrate complex during catalysed reaction fie A Energy dagamoshow he dfleence beeen an uncatased and a catahsed reaction How do enzymes work? To lower the activation energy and catalyse a reaction, enzymes form a complex wit the substrate nbstates ofthe reaction. A simple picture of enzyme action in a catabolic reaction is: substrate + enzyme = enzyme/substrate complex = enzyme + products 58‘Once the products of the reaction are formed they are released ‘and the enzyme is free to form a new complex with more substrate. How does this relate to th structure of the enzyme? ‘The ‘lock-and-key hypothesis’ gives usa simple model that helps us understand what happens (ee fig B). With the globular protein structure of each enzye isan area known as the active site thar has a very specific shape. Only one substrate or type of substrate wil ft che shape of the gap, and i is this that gives each ‘enzyme its specificity. Just as a key fis into a lock, so the enzyme ‘and substrate slot together to form a complex. ‘The formation of the enzyme/subsirate complex lowers the activation energy of the reaction. The active site affects the bonds in the substrate, making it easier for them to break, and the reacting substances are brought close together making it easier {or bonds to form between them. Once the reaction is complete the products are no longer the right shape to stay in the active site and the complex breaks up, releasing the products and freeing the ‘enzyme for further catalytic action. substrate This molecule cannot ft into > the active site ; So this enzyme cannot catalyse a active site aalparie molecule products enzyme/substrate complex formed @ \ 99 fig The lockeand-iey hypethes inderine our understanding othe ‘The lock-and-key hypothesis fits most of our evidence about ‘enzyme characteristics. However its now thought to be an ‘over simplification, Evidence from X-ray crystallography, chemical analysis of active sites and other techniques suggests that the active site of an enzyme is not simply a rigid shape. In the induced-fit hypothesis, generally accepted as the best current ‘model of enzyme action, the active site stil has a distinctive shape and arrangement, but it is a flexible one. Once the substrate enters the active site, the shape of the site is modified around it to form, the active complex, Once the products have left the complex the ‘enzyme revert to its inactive, relaxed form until another substrate molecule binds (see fig C) active site is not fully complementary shape to substrate \ ntl substrate fits into it products Guid fig The induced-ft theory of enzyme action proposes that he etaljic ‘groups ofthe active se ate not brought nto thar mast activ pes tone Uni a cubstate & bound to the ste, nducng a change in shape Measuring reaction rate When cients ee investigating enaymes and how they act as catalysts, they Requentiy measure the reaction rate or example one practical way of demonstrating the effect of an enzyme on @ Teection is to mesure the rate of the reaction with end without the eye, Using this method it has been shown tat when rea breakdown is catalysed by urease extracted from the jack bean, the rate of the reaction increases by a factor of 10. Enzymes are such eficientcatatyst that they generally increase reaction rates by factors fom 10°10 10% This i why ony tiny amounts of most craymes are needed Much of the evidence for the structure of enzymes and the way tis relates to their functions comes from practical investigations into the effect of different factors on the rate of enzyme-catalysed reactions. To investigate the way a factor affects the rate of reaction, biologists measure the initial rate of reaction cach ‘ume the independent variable is changed. Every other factor must bbe kept the same so that any changes are the result of changing the one variable. Ieis important to provide a large excess of substrate in enzyme experiments, unless the effect of substrate concentration is under investigation. The intial rate of reaction is when the reaction [proceeds at its fastest rate. This gives the maximum reaction rate {for an enzyme under particular conditions, for example changing pH, temperature or substrate concentration, 59)What do we know about enzymes? ur current model of enzymes is that they are globular proteins {see Seetion 1.2.4), which contain an active site that i vital 0 the functioning of the enzyme. The active site is a small Gepression on the surface ofthe molecule thathas & specific shape because ofthe “way the wihole large molecule is folded. Anything affecting the shape of the protein molecule affects its ability to doit job, which indicates that the three-dimensional (3D) nature ofthe molecule is important to the way it works. change in shape changes the shape ofthe active site as well~ and so the enzyme can no longer function, Enaymes change only the rate of a reaction. They do not change or contribute to the end products that form, or affect the equilibrium of the reaction. They act purely as catalysts and not as modifying infuences in any other way. Evidence for the relationship between the structure and functions of enzymes Cbserving the factors that affect the rate of enzyme activity gives an insight into the relationship between the structure of an enzyme and the way it functions. + Enzymes speed up reactions to such an extent that only ‘minute amaunts of them are needed to catalyse the reaction of many substrate molecules into products. This is described by the molecular activity or turnover number of an enzyme, which measures the number of substrate molecules transformed per minute by a single enzyme molecule. The nurmber of molecules of hydrogen peroxide catalysed by the enzyme catalase extracted from liver cells has been reported as 6 x 10° in 1 minute, Most enzymes would catalyse thousands of molecules per minute rather than millions. I every enzyme ‘molecule is involved in a reaction. it will not go any faster unless there is an increase in the enzyme concentration. In other words, enzyme controlled reactions are affected by the concentration of the enzyme. + Enzymes are very specific o the reaction that they catalyse. Inorganic catalysts such as platinum frequently catalyse many different reactions, often only at extremes of temperature and pressure. In comparison, some enzymes are so specific that they will catalyse only one particular reaction. Others are specific toa particular group of molecules that are all of similar shape, or to a type of reaction that always involves the same groups. This suggests that there is a physica ste ‘within the enzyme with a particular shape into which a specific substrate will fit + ‘The number of substrate molecules present (the concentration of the substrate) affects the rate of an enzyme-catalysed reaction. Take a simple reaction where substrate A is converted to product Z. Ifthe concentration of A increases, the rate of the enzyme-catalysed reaction A — Z increases — but only for 80 long, Then the enzyme becomes saturated —all of the active sites are occupied by substrate molecules ~ and a further ‘increase in substrate concentration will not increase the rate of the reaction further (see fig D). At tis point only an increase in enzyme concentration will increase the rate of the reaction, V4, maximum rate of reaction Vaye approached af al sites become occupied. "At lower substrate coneentrations, some enzyme molecules have their active sites ree Rate of reaction (¥) —> ‘Substrate concentration —> D The efecto berate concaintion on an ensyecatsyead schon showing how tie enzye becomes sau ated wih substale molecules + Temperature affects the rate of an enayme-catalysed reaction ina characteristic way. Temperature affects all reactions ‘because the number of successful collisions leading to a reaction increases at higher temperatures. The effect of temperature on the rate of any reaction can be expressed as ‘he temperature coefficient, Qo This is expressed as rate of reaction at (+ 10)°C 1 = Tate of reaction at x°C Between about 0°C and 40°C. 0,» for any reaction is 2—the rate of the reaction doubles for every 10°C rise in temperature. However, ouside this range, Q,, for enzymme-catalysed reactions in human beings decreases markedly, whilst Q for other reactions changes oniy siowiy. The rate of enzyme-catalysed reactions in human beings falls as the temperature rises, and at about 60°C the reaction stops completely in most cases. At temperatures over 40°C most proteins, including most enzymes, star to lose their tertiary and quaternary structures they denature. When enzymes denature, the shape of the active site changes and so they lose their ability to catalyse reactions, There are some exceptions to this rule, For example the enzymes of thermophilic bacteria which live in hot springs at temperatures of up to 85°C, are able to work at very high temperatures. They are made of temperature-resstant proteins that contain a very high density of hydrogen bonds and disulfide ‘bonds, which hold them together even at high temperatures (sce Section 1.2.4). However, the optimum temperature of the enzymes of many organisms, including cold water fsh and ‘many plants, is much lower than 40°C, ‘The rate of reaction doubling with each 10°C risein temperature Optimum temperature ~ here the reaction proceeds as fast as possible. ‘The enzyme loses its ability to catalyse the ‘Temperature —> fig The effect cl temperature on the rate of a ypial enzyme-catahsed reaction. Al other factors must be kept corsaEN + pH also has a major effect on enzyme activity by affecting the shape of procein molecules Different enzymes work indifferent ranges of pH, because changes in pH affect the interactions between R groups, for example hydrogen bonds and ionic bonds that hold the 3D structure of the protein together. The ‘optimum pH for an enzyme is not always the same as the pH of its normal surroundings. This seems to be one way in ‘hich cells control the effects of their intracellular enzymes, increasing or decreasing their activity by minute changes in she pH 3 . 6 3B elt d ep . 6 oH 3 cholinesterase z 3 3 © elt fig FDiferent enzymes work bs at clferent pH les. Al ater Face be kept constant Did you know? RuBisCo - a key but inefficient enzyme for ite Ribulose bisphosphate carboxylase/oxygenase (known as RuBisCo) is vitally important in photosynthesis. tis the enzyme that catalyses the fixing af carbon oxide from the airinto the biochemistry of sugar formation, Without this enzyme, lifeas we know it would not text But RuBisCo i a remarkably inefficient enzyme. “+ Most enzymes catalyse about 1000 reactions per second, RuBisCo ‘only catalyses about 2, Plant cells overcome this by making very large quantities of RuBisCo - about haf of the protein in a photosynthetic plant cells this enzyme, + The activesite of most enzymes is very specific. RuBisCo binds to carbon dioxide molecules in photosynthesis but it can aso bind ‘to oxygen molecules in a process called photorespiration. It affinity for carbon dioxide is about 80 times greater than for ‘oxygen - but there is much more oxygen available so about 25% ‘oF RublsCo binds to oxygen Scientists believe RuBisCo evolved in an atmosphere containing very litle oxygen and much more earhon dioxide than it does today 0 ‘oxygen: binding was nota disadvantage at the time and so itwas not selected against in evolution, 1 (@) summarise the characteristics of enzymes, (©) Explain how each characteristic of enzymes provides evidence for the induced: fit hypothesis, 2 Plan a practical investigation into the effect of temperature on enzyme activity Key definitions Activation energy isthe energy needed fora reaction to get started [substrate is the molecule or molecules on which an enzyme acts. The lock-and-key hypothesis isthe model that explains enzyme action by an active stein the protein structure that hasa very specific shape. The enzyme and substate sot together to forma complex as a keys in a lock, [An active site is the area ofan enzyme thathas a specific shape into hich the substrate(s) of a reaction ft The induced-fit hypothesis a modified version of the lock-and key hypothesis for enzyme action where the active site fs considered tohave a more flexible shape. Once the substrate enters the active site, the shape ofthat ste is modified around it to form the active complex. Once the products have left the complex, the enzyme reverts to its inactive, relaxed form, ‘The inital rate of reaction isthe measure taken to compare the rates of enzyme controlled reactions under diferent conditions. ‘Molecular activity turnover number) is the number of substrate ‘molecules transformed per minute by a single enzyme molecule, The temperature coefficient (Qj) is the measure ofthe effect of temperature on the rat ofa reaction. aaaa tala ed ited a) By the end of this section, you should be able to.. © describe how enzymes can be affected by competitive, non-competitive and end-product inhibition We can learn more about enzymes and how they work by looking at evidence from substances that stop the enzymes from working “These are called enzyme inhibitors. When we look at how inhibitor molecules interfere with the catalytic powers of an enzyme, we can get more evidence about the way they carry out their functions. There are two main types of inhibition, reversible inhibition and irreversible inhibition Reversible inhibition of enzymes When an inhibitor affects an enzyme in a way that does not ‘permanently damage it, this is reversible inhibition, When a reversible inhibitor is removed, the enzyme can function normally again, Reversible inhibition is a cornmon feature of metabolic pathways, and it provides a key way of controlling reactions, as ‘you will see. There are rwo major forms of reversible inhiicion competitive inhibition anc non-competitive inhibition. Competitive inhibition In competitive, reversible inhibition, the inhibitor molecule is similar in shape to the substrate molecule. It competes with the ‘substrate for binding atthe active sites of the enzymes, forming an enzyme/inhbitor complex. Ifthe amount of inhibitor is fixe. the percentage of inhibition can be reduced by increasing the substrate concentration. The two molecule types are competing forthe same active site, The more substrate molecules there are, ‘the les likey its that inhibitor molecules will bind tothe active site ‘Non-competitive inhibition In non-competitive reversible inhibition, the inhibitor may form a complex with either the enzyme itself or with the enzyme/ substrate complex. This shows that the inhibitor is not eompeting forthe active site, I joins to the enzyme molecule elsewhere. This is confirmed by the fact that only the concentration of inhibitor affects the level of inhibition. The concentration of the substrate rakes no diference to how much inhibition occurs. The best ‘model for how this inhibition works is thatthe presence of the inhibitor on the enzyme or enzyme/substrate complex deforms or changes the shape of the active site so tha it can no longer catalyse the reaction, Fig A shows the differences between competitive and non-competitive inhibition, 62 €,—-@ f —- Ba: A Competitive inhisors compentive nhbors uibstrate Inhibitor Irreversible inhibition of enzymes In irreversible inhibition the inhibitor combines with the enzyme by permanent covalent bonding to one of the groups vital for catalysis to occur It changes the shape and structure of the molecule in such a way that it cannot be reversed the enzyme is inactivated permanently {reverse inhibition tends to occur ‘more slowly than the other forms of inhibition, but its effects are ‘much more devastating and are never used within the cells to contro] metabolism, Arsenic, cyanide and mercury are poisonous because they ‘exert irreversible inhbition on enzyme systems. Some of the nerve gases used in chemical warfare also work in this way. ‘They combine with and completely inactivate enzymes such as acetyl cholinesterase that break down chemicals used to transfer impulses from the nervous system ta the muscles of the body ‘The normal function of aceryicholinesterase is ta destroy the neurotransmitter called acetyicholine at the junctions between neurones and muscle cells. It does this as soon as an impulse hhas been passed from a nerve to 2 muscle, When the enzyme is inhibited the impulse continues, The muscles ga into prolonged spasms causing death because breathing and swallowing become impossibleEN End-product inhibition and the regulation of the cell {As you know, hundreds of chemical reactions are going on within a cell at any one time, their rate controlled by the action of enzymes. A similar number of reactions occurring in a very small space in alaboratory would, without doubs, end in total chaos if not a large explosion. $o how do cells ‘manage their reactions in such a controlled way? There are many factors involved. Membrane ‘compartments keep reactions apart, Variations in pH can change the rate of enzyme-catalyse: reactions, and the amount of substrate available is another mechanism at work. But one of the most important methods of control is that exerted by the regulatory enzymes. Regulatory enzymes citen have a site, seperate from the active site, to which another molecule can bind and bring about non-competitive inhibition. They are widely found in complex metabolic pathways such as photosynthesis and respiration, In end-product inhibition the regulatory enzyme is found near the beginning of the pathway Itis inhibited by one of the end products of the chain. There are some very important examples of end: product inhibition in the pathways of cellular respiration in all organisms, Phosphofructokinase (PFK) ia an enzyme involved in the production of ATP in the process of glycolysis in cellular respiration (sce Book 2, Section 5.1.2). PPK contwols the rate of respiration by end-product inhibition. It is inhibited by ATR which binds non-competitively and changes the shape of the active site, If the ATP ‘concentration goes up, PFs inhibited and cellular respiration slows down, As ATP levels fall, ATP ‘molecules detach from PFK and the enzyme becomes active again, Rates of celluar respiration ~ and. s0 ATP production ~ increase, B |— [ec |— a) erent 1 Whats theaference between reversible and ineverible enzyme inhibition? 2. what are he main dferences between everile competitive ard non-compete Inhibiton in enzymes and how des tse the contol of reactions within a el? Enzyme inhibitors are substances that slow down enzymes or stop them from working Reversible inhibition is inhibition ofthe action ofan enzyme by an inhibitor that does nct permanently affect the functioning ofthe enzyme and can be removed from the enzyme. It's often used to control reaction rates within a cell Irreversible inhibition is inhibition ofthe action of an enzyme that is permanent and cannot be undone. Itis never used within ces to contr the rate of reactions ‘Competitive inhibition is inhibition in which the inhibitor molecule is similarin shape to the substrate molecule and competes with it for the ative site ofthe enzyme (afected by both inhibitor and substrate concentrations). 'Non-competitive inhibition is inhibition in which the inhibitor does not compete forthe active site but forms a complex withthe enzyme or enzyme/substrate complex and changes the shape ofthe activesite soit ean no longer catalyse the reaction (affected only by concentration of inhibitor) Regulatory enzymes are enzymes that have a site separate to the active site where another molecule can bind to have either an activating or inhibitary effect, End-praduct inhibition is 2 contro system in many metabolic pathways in which an enzyme at the beginning ofthe pathway is inhibited by one ofthe end products of the reaction 8RAW ENZYMES - REALLY? ‘The enzymes made by the cells of your body are vitally important. Inside your cells, they contral all the reactions of life. Qutside your cells they ere particularly important in the digestion of your food. ‘The internet is a great source of information but not all of itis reliable, Read the following texts ‘about food and erzymes, based ona number of different websites promoting ‘good health, Site 1 ‘Each person is bom witha limited enzyme-producing capacity, Your Life expectancy depends on how well you preserve this enzyme ‘potential. You need to take in enzymes from the food you eat. Tr you don’t take in enough enzymes, i imposes a grea siran on your ‘igestive system because it has to produce all the enzymes you ‘need, This in tum reduces the numbers of enzymes available for the metabolic reactions taking place in yous cells ~ and this is the root ‘cause of most chronic health problems, The solution is simple: eat at least 75% of your food raw to make use of the enzymes in the food, ‘eat Jess, chew your fod well and don’t chew gum! Site 2 When food is cooked, enzymes are destroyed by the heat. Enzymes help us digest our food. Enzymes are proteins, and they ‘work because they have a very specific 3D structure in space. ‘Once they are heated much above 118 degrees, this structure can ‘be changed so they no longer work. Cooked foods contribute 10 chronic illness, because their enzyme content is damaged and sowe have to make our own enzymes to process the food. This uses up valuable metabolic enzymes. I takes a lot more energy to digest cooked food than raw food ~ the evidence being that ‘ra food passes through the digestive trict about 50% faster than ‘cooked food. Fating enzyme-dead (cooked!) foods overworks and ‘eventually exhausts your pancreas and other organs. Many people ‘progressively lose the ability to digest their food after years of | ‘eating cooked and processed food. ‘Where else will encounter these themes? Site 3 Enzymes are an essential part ofa healthy diet. As an expert explains, “Science cannot duplicate enzymes. Only raw food hhas functional living enzymes. The chain reaction generated by cenzymes helps to send fats to where they are needed in our body, instead of being stored fig The cls of raw frit and vegebles are fl of enzymes - but how much use are they 10 you?CO eo Let us start by considering the nature of the writing in these articles: [rere 18 auestion your answer mange cee ( Seem re | [Sooner eo | Now let us have a look at the biology: Your knowledge of biochemistry is now at a level that allows you to read this article with a scientific mind! Enzymes are vital for life. Aheathy diet provides your body with the materials it needs to make enzymes but you donot directly use the enzymesin the food that you eat Prepare a three minute talk fora debate tiled 'Raw food - the only healthy way to support your enzyme: Choose whether you want to support this idea or oppose it. Focus an the biology of enaymes and of the compounds that make up your food. Whichever side you choose your argument must be backed up by good scientific evidence. { Consider what you fs | teamed about anya srt ek lene | cel and inte cgpoing ontenst onriones | inching peopl te an Meng bub mate sue tha | Your sources are reliable) _/ (© tase oma marber of ifsc websites promoting “goo healt14 Exam-style questions 1 Amylase is an enzyme that breaks down starch to maltose, A student carried out an investigation to determine the effect of copper ions on the activity ofthis enzyme. She added cifferent concentrations of copper ions and timed hox« long it took the amylase to break down starch, “The results of this investigation are shown in the graph below, 8 Time for starch breakdown’ 4 ‘minutes "Od 8 12 16 20 a 28 22 ‘Concentration of copper ions/ arbitrary units (@) Describe a test that could be used to show that starch has ‘been broken down. Gl (b) Describe the effect that an increase inthe concentration of copper ions has on the activity of amylase (3) (c} The student suggested that the copper ions were acting as an active site-directed inhibitor at concentrations above 4 arbitrary units. Explain what is meant by the term active site-directed inhibition. 8) (a) The student then investigated the intial rate of reaction using amylase and different concentrations of starch. She did this frst with copper ions present and then with no copper fons present. The results are shown in the graph below Initial rate of reaction/ arbitrary units o 2 4 6 & ‘Starch concentration/atbitrary units (i) Explain why the initial rate of reaction was measured ‘inthis investigation 2) {i) State why the results do not support the hypothesis that copper fons are an active site-directed inhibitor of amylase. (1) [Total: 12] 2 (a) The graph below shows the change in energy that takes, place during a chemical reaction | Energy| Energy of reactants, Time — (i) With reference to enzyme activity explain the meaning, of each of the following terms, + Activation energy = Catalyst (4) {i) On the graph above, draw the energy changes that ‘would take place if the same chemical reaction was catalysed by an enzyme. re{) An experiment was carried out to determine the effect of temperature on the activity of a protein-digesting enzyme (@ protease). Solutions of the protease were incubated ‘with 2 protein called gelatine at three temperatures: 20°C, 30°C, and 40°C. The concentration of amino acids were measured over a 48-hour period. The results are shown in the graph below 240 20 180: 150 Amino acid concentration/ 120: arbitrary units 90. 60: 30 ot 62 630 «050 ‘Time of incubation hours () Name the type of reaction catalysed by this protease, ie {ii) Name the bond broken by the protease. fy (ii) Caleulate the mean rate of production of amino acide fat 40°C during the first 36 hours of incubation, Show your working and give your answer in arbitrary units ar Q (jv) The optimum temperature for this reaction is 30°C. Explain the shape of the curve at this temperature (2) [Total: 12] 3 Trypsin sa protease enzyme that catalyses the breakdown of proteins. An investigation was carried out to study the effect of pH on the activity of trypsin. The source of protein in this investigation was milk powder mixed in distilled water This, gives a white, cloudy suspension. ‘A 2% solution of trypsin was prepared and placed in a waterbath at 45°C. A 10% suspension of milk powder was prepared separately and 3 cm? samples of this suspension ‘were mixed with 3 cm! of a pH buffer solution and placed in waterbath at 45°C. Buffer solutions between pH 5 and pH 9 were used. When all the mixtures had reached a temperature of 45°C. 0.5 cm’ of the trypsin solution was added to the suspension and the time taken for the suspension to clear was recorded, ‘The results of this experiment are shown in the table below pH of suspension ‘Time taken for suspension to clear/min 5 1082 é 6.68 7 138 a ort @ 1a 10 7.80 (@) (9 Explain how an enzyme, such as trypsin, digests (breaks down) the protein in the milk powder (31 (i) Describe why the cloudy suspension goes clear when mixed with the enzyme. i) (b) (Use the information in the table to describe the effect, of pH on the activity of trypsin. 2) (i) Explain how pH affects the activity of enzymes [3] (c) Explain why the experiment was carried out in a water bath at 45°C. 2) (Total: 11]In October 1951, Henta Lacks young 31 -et-old American back woman ded fan agesie cance othe conic Before she ded docs ook ape oer cll whch became the Wx ura cs elnino RE NER oP ere acc barca are nil ae ete wees cultured HeLa cals have layed an inporant arin cellbology and meal Te eae ean RGeII TEE eyes ine la call ep ican relaly and they have waved ey have TE in dare ecttet are Oe Uk Inthis chap youve be ds ee te pale ey Mestre coud not een fe most cal and g0 YoU wien sre ow cron Ae eet By looking at the mary cifferent types of organelles within a cell you will discover both their structure, thelr function and how they work together. Key o sare the mitochondria ~ so important they at enables them to divide independently. This is where the reactions of cellular ures found in animal cells ~and a few oftheir own, You will be these Features, which highlight ata cellular level some of the major Use scales for measuring (eg. gratcule to measure sizeof cel) Make order of magnitude manipulate the magnification formula: ‘magnification = size of imag al object) Use and manipulate equations, including changing the subject ofan equation (eg. magnif Caleulate the circumference, surface areas and volumes of regular shapes (eg. calirs TESA ence eee Ty Sate et rete eee eee oer Rte Be eet renee ecru Pee eer ror ate “The structure of viruses ~ how they differ from all other living organisms and how they ceproduce in other cells ede ey Dee Mitotic cell division producing two identical daughter cells eens eee ere ee eas efrercil fied Giger Meictc eal division asa source of genetic variation Pe ee een) pteadlacaiehlaell AP ceo eeraamiparier ices. 6 Cae ee uu Pea ern cr et ee eet Se ea SAR aur How electron microscopy has increased our one understanding of subcellular structures See ee ee ere ry ee Ts eater tae oe een onan ar ven Cee eee eno The cells ofthe immune system (A evel) ri Cee ee eee ou) SR ee eens microscope and the electron microscope Se eens Ls ‘microscope (including staining) and the electron cree’ The difference between magnification and corny Seen eet gee eet ese ea sett pees The importance and structure f cell membranes The main membrane-bound organelles of animal ere a net teres Poet see eet ee euret eres ea peer eee eer nea ces pero e arty See ee ee ere and plant cel, including cell walls, chloroplasts, ‘vacuoles and tonoplasts Cyfe) oxT aval By the end of this section, you should be able to.. © explain cel theory as a unifying concept that states that cells are a fundamental unit of structure, function and organisation in alliving organisms (© describe how magnification and resolution can be achieved using ight and electron microscopy © explain the importance of staining specimens in microscopy Cells are discussed in the media on an almost daily basis in relation to topics such as cancer, stem cells and DNA testing, However in spite of the fact thar we have known about cells for ever 300 years, most people have only a vague idea about what they are and how they function Discovering cells Robert Hooke (1635-1703), an English architect and natural philosopher designed and put together Cone ofthe first working optical microscopes. His observations were published in his book Micegraphia in 1665. Amongst the many objects he examined were thin sections of cork, made up of tin, regular compartments thathe called cell, a they remind him of the monks’ cells in a monastery in 1676 Anton van Lecawenhoek (1632-1723) a Dutch draper who ground lenses in his spare time to check the "weave of is fabrics, used his lenses to cbserve a wide variety of living unicellular organisms in drops of water which he called ‘animalcules’. At the same time the English plant scientist Nehemiah Grew (1641-1712) was one of the fist scientists to publish accurate drawings of "issues. By the 184Ds we understood that cells re the basic units of fe, an idea that was first expressed by Matthias Schleiden (1804-188: and Theodor Schwann (1810-1882) in their cell theory of 1839. Cel theory isnow accepted as a unifying concept in biology I states that cells area fundamental unit of structure, function and orgenisetion in all living organisms. Improvements in the quay of lenses, new staining techniques andthe introduction of new technologies such as electron and confocal microscopes, have allowed us to see celsin increasing detail and so develop our understanding of both their structure and function 1 key to understanding biology. 70re ED Microscopes \We can see some cells easly with the naked eve, for example the ovum in an unfertlised bird's egg is, 2a single cell, But we need some kind of magnification to enable us to see most cells ‘The light microscope or optical microscope has been the main tool for observing cells ever the years and itis stil widely used. A good light micraseope can magnify to 1500 times and still give a ‘lear image. At this magnification an average person would appear co be 2.5 km tall Since the mid-twentieth century the electron microscope has given scientists an even greater insight into the inner workings of cells. An electron microscope can give a magnification of up to 500.000 times, making an average person appear over B30 km tall Didyouknow? 0 Magnification and resolution are the two features of any microscope that determine how clear the image i. «Magnification is a measure of how much bigger the image you sees than the real object, 2g 40, 1000 or «500000. + Resolution or resolving power is a measure of how clase together two objects can be before we see. them as one. For example the recoution of the naked eye is around 0.1 mm. Two ebject closer together than 0.1 mm cannot be seen as separate objects. The resolution of alight microscope is around 02 wm (200 nm), and the resolution of an electron microscope is around 0.1~1 nm, The light microscope ‘A specimen or thin slice of biological material is placed on the stage of a light microscope (see fig B) end illuminated from underneath, either by sunlight reflected with a mirror or by a bull-in light source. The objective lens produces a magnified and inverted image. which the eyepiece lens focuses at the eye. The total magnification of the specimen is calculated magnification cf magnification of, total cbjective lens eyepiece lens. = magnification eg 10 x “10 100 eyepiece lens, Diverging light rays enter the eye. They are perceived as coming from the magnified image objective lens. specimen stage apparent size of specimen after magnification $B Light pases through the specimen and an though the lenses to guean image tha & magrifid and upside dow nfig € A good ight micrograph of tissue wh airing that shows Up the diferent ypes cfcats can provide us with alot of Informations demansrared 22 bytheserten trough ovarian a eS Using the equation image size ~ actual size x magnification You can work out the size of a specimen by measuring it under the microscope, as long as you always. record the magnification you are using. For example the diameter of a cell measured under the light merescope at magnification »400 is 1 mm Multiply 1 by 1000 to convert mm to pm: 11090 = 1000 ITE SE actual size ‘magnification “a9 7254" ‘You can look at living organisms, tissues and cells under the light microscope. However, most of the specimens will be dead stained. specially preserved and sectioned (very thinly sliced) before they are mounted on a slide. The staining is used to make i easier to identy particular types of cell, or particular parts of the cells, under the microscope. Some of the stains you may come aero include: + haematoxylin ~ stains the nuclei of plant and animal cells purple, bhie or brovm + methylene blue —stains the nuclei of anirnal cells blue + acetocarmine ~ stains the chromosomes in dividing nuclei in both plant and animal cells + iodine ~ stains stareh-contaning material n plant cells blue-black ‘There are big advantages to using ight microscopes, but there are some disadvantages too: of the light microsc = Can see living plants and animals, or parts of | Preservation and staining tissue ean produce them, direcly. Ths s useful in tse and allows | artefacts inthe tissues being observed, so what yeu to compare prepared slides with living tissue. | ie see may be the result of preparation rather + Relatively cheap so are available in schools and | _ than a true representation ofthe living tissue. universities, hospitals, Industral labs anc research | «Limited powers of resolution and magnification, labs, + Relatively light and portable sowe can use them almost anyivhere, eg identfying malaria in the field Developments including the confocal microscope mean the information we can get from light mieroscopes continues to increase. The electron microscope “The elect microscope uses a beam of electrons o form an image The electrons are scattered by the specimen in much the same way as ight is scattered in the ight microscope. In an electon microscope the electrons efectely behave lik light waves wit every ny wavelength Electomagnetc or electrostatic lenses focus the electron beam to form an nage Resolving pover increases asthe wavelength gets smal, o te electron micrencope can resolve deal down fo fess than 0.00001 ym, about 10000 times better than the light microscope. For the electron microscope to work, the specimens have to be in ¢ vacuum, so they are always dead, The preparation of a specimen for the electron microscope is a very complex process that may involve chemical preservation, freeze drying, fteeze fracturing, removing the water (dehydration), ‘embedding, sectioning and mounting on a metal grid. Specimens far electron microscopy are often stained using heavy metal ions such as lead and uranium. This is not to identify particular tissues, but to improve the scattering of the electrons and make greater contrast inthe image, making it learer and easier to interpret. The image is displayed on a monitor or computer screen.re ton source Be very clear about the difference between magnification and resolution, Make sure you are able to calculate the size, magnification or image size of any specimen, electromagnetic lens ‘There are two main types of electron micrographs. Transmission electron micrographs (TEMS) are two-dimensional (2D) images like those from a light microscope. Scanning electron micrographs (SEMs) have a lower magnification, but are three-dimensional (8D) and can be very striking, Sometimes electron micrographs are given false colours to make it easier to identity tae different cells, but these are not stains. They are added after the image has been taken, electromagnetic lens There are big advantages to using electron microscopes, but there are some disadvantages too! ane Disadvantages of the electron microscope = Huge powers of magnification and resolution. = All specimens are examined ina vacuum - air > electromagnetic lens Many details of cellstructure have been seen for would scatter the electronsand make the image the frst time since they were developed. ofthe tissue fuzzy ~ 50 iis impossible to look at living material image Specimens undergo severe treatment that spayed likely to result in artefacts. Preparing specimens ‘on a monitor for the electron microscope is very skilled work Extremely expensive. Large, have to be kept at a constant temperature and pressure and need to maintain an internal ‘vacuum. Relatively few scientists outsice research laboratories have easy access to such equipment. the specimen and on Why i high magnification alone not enough to give us biological details of cells? 2 bon ight ard elecuon micrographs ca be bight coloured. Explain the iferences and simiaies betwen he way colour outed ligt and eon mioncpy. 3 A student measured the diameter of three cells ofthe same type under the microscope. Measurement 1 ‘was taken with a magnification of 40, and measurements 2 and 3 with a magnification oF «100, ‘Work outthe mean diameter ofthe cell, Measurement =Smm — Measurement2=12mm Measurement 3= 1 mm {ge ‘tanemisson election nicograph of cell ges yous Key definitions much more deal norma han the ahem fee Aight microscope (optical microscope) is ool that uses a beam oflight and optical lenses to magnify specimens up to 1500 times lifesize. ‘An electron microscope stool that uses a beam of electrons and magnetic lenses to magnify specimens ‘up te 500000 times lifesize Magnification isa measure of how much bigge the image you see than the real object. Resolution (resolving power) is a measure of how clase together two objects can be before they ae seen ‘Transmission electron micrographs (TEMs) are micrographs produced by the electron microscope that give 2D images ike those from alight microscope, but magnified up to 50000 times, Scanning electron micrographs (SEMs) are micrographs produced by the electron microscope that have 4 lower magnification than TEMs, but produce a 3D image. BCell membranes By the end of this section, you should be able to.. © define eukaryotic and prokaryotic cells (© recognise that cell membranes are common to eukaryotes and prokaryotes, @ explain how the structure and properties of phospholipids relate to their function in cell membranes Most of the familiar organisms in the world around you have the same sort of cells. Animals, plants, protoctists, algae and fungi have cells with the genetic material contained in a ‘membrane-bound nucleus. ‘The cells also contain a number of other membrane-bound organelles such as mitochoneiria and chloroplasts. These organisms are called the eukaryotes. But there is another ancient group of orgenisms, including the bacteria and cyanobacteria, known as the prokaryotes. They have cells of a very different type that lack much of the structure and organisation ofthe eukaryotic cells. but they do have a cell surface membrane. You will look st both eukaryotic and prokaryotic cells in this topic, but you will begin by studying the structure of the membranes that are common to all Membranes in cells ‘There are many membranes within cells, such as those that ‘surround organelles lke the nucleus and mitochondria, But the ‘most cbvious membrane is the cell surface membrane. also known, as the outer cell membrane, which forms the boundary of all cells ~ controling what passes into and out of the cell and allowing the fiuids either side of it to have different compositions. Membranes ‘within cells make it possible to have the right conditions for a particular reaction in one part of a cell and different conditions to ‘suit other reactions elseviere inthe same cell. Membranes perform many other functions toa. Many chemical processes take place on membrane surfaces. For example, the reactions of respiration in eukaryotic cells take place on the inner ‘mitochondrial membrane. Enzymes and any other factors are held closely together so thatthe reaction processes can proceed smoothly, The cell surface membrane must also be flexible to allows the cell to change shape very slighty as its water content changes, or quite dramaticaly for example when a vitite blood cell engulfs a bacterium. Chemical secretions made by the cel are packaged into membrane bags known as vesicles, so some membranes must be capable of breaking and fusing together readily 74 fig One ofthe functions ef this stack of membranes ina lant al the Golp appeats) 1 pactage secretions into vesicles tut one ofthe ‘memarane-rch organelles you can find ina eularyeic cell, The structure of membranes (Our current mode! of the structure of membranes has been ‘worked out over many years. The model developed as microscopy improved. from light to electron and then scanning electron microscopes. In time there may well be further refinements to the model presented here, but the overall picture seems unlikely to change dramatically. The membrane is made up mainly of ‘wo types of molecules - lipids and proteins ~ arranged in a very specific way. The phospholipid bilayer ‘The lipids in the membrane are of a particular type called polar lipids. These are lipid molecules with one end joined to a polar ‘group Many of the polar lipids in the membrane are phospholipids, ‘with @ phosphate group forming the polar part of the molecule (see Section 1.2.3). With water ar aqueaus solutions an each side, Phospholipid molecules form a bilayer with their nydrophilic heads pointing into che water while the hydrophobic tals stay protected in the middle. This structure is known as a unit membrane. However, a simple lipid bilayer alone would not explain either the microscopic appearance of membranes or the way in which they behave. A simple lipid bilayer allows fat-soluble organic molecules to pass through it, but many vital chemicals needed in cells are ionic, Whilst these dissolve in water they cannot dissolve in or ‘passthrough lipids, even polar lipids They can enter cells because the membrane consists not only of lipids, bur also of proteins and other molecules. The membrane proteins ‘Tae best model of a membrane we have today sees the basic bileyer of phospholipid asa uid system, with many proteins and other molecules floating within it lke icebergs whilst others are fixed in place (S22 fig B). The proportion of phospholipids containing unsaturated fatty acids (see Seetion 1.2.3) in the bilayer seems to affect how freely the moving proteins float about inthe membrane. The more unsaturated fry acids, the mare fuid the membrane. Many of the proteins have a hydrophobic part, ‘wich is buried inthe lipid bilayer, and a hydrophilic part, which‘can be involved in a variety of activities. Some proteins penetrate all the way through the lipid, while others only go part of the way through the bilayer. ‘One of the main functions of the membrane proteins isto help substances move actoss the membrane. The proteins can form potes or channels ~ some permanent, some temporary — that allow specific molecules to move through. Some of these channels ‘can be open or shut, depending on concitions inthe cell. These are known as gated channels. Some of the protein pores are active cartier systems using energy to move molecules, as you will see later Others are simply gaps in the lipid bilayer that allow ionic substances to move through the membrane in both directions. Proteins may act as specific receptor malecules ~for example, ‘making cells sensitive to a particular hormone. They may be ‘enzymes, particularly on any internal cell membranes, to control reactions linked to that membrane, Some membrane proteins are glycoproteins proteins with a carbohydrate part added to the molecule. These are very important on the surface of cells as part Of the way cells recognise each other ‘This model of the floating proteins ina lipid sea is known as the fluid mosaic model and was list proposed by S. Jonathan Singer (1924-) and Garth Nicholson (1943-) in 1972, q 7 A ; — ui me 3 phospholipid integral Nore protein (fycrophilic channel) fg wether acting 2s tho bounday fa calor as pat ofits renal make-up, he compies sructuze of the membrane s clos linked ois wide variety of Didyouknow? 0 Evidence for the fluid mosaic model Techniques such a X-ray fraction and advanced electron microscopy have added to our knowledge of the structure of cel membranes, giving us more detals ofthe layers, the pores and the cartier molectles However, even under the electron microscope, cell membranes are very smal. Microscopes have helped scientists develop our current membrane model, but other techniques are alo important. We can Identify proteins that appear to have a specific function of transporting particular ions into or out of the cel through the ‘membrane. Cystic fibrosis fs a genetic disease that affects transport across the membranes ofthe glands, the digestive system, the respiratory system and the reproductive system. If an individual inherits faulty allele (variant from each parent, the protein needed to transport chloride fons across the membranes (cyte fibrosis, twansmembrane regulatory channel protein) doesnot form propery. This affects the movement of water out of the cell and leads tothe’ formation of sticky mucus, which can lead to serious chest infections, ligestive problems and infrilty. identifying protein channels in the membrane that have avery specific function that can be measured helps to confirm our madel of cell membrane structure and function. {fig The membrane pores trough which mRNA leaves the nucleus ate clea visible inthis fesre-etched secon ‘micrograph ofthe nuclear membrane ofscel Summatise the main Functions of membranes in cells, Ni ef Which kinds of molecule make up the structure of a membrane and how do their properties affect the properties of the membrane fel? 3. Discuss why the lecble structure ofthe cell membrane well adapted forts functions nthe cel Key definitions COrganelles ae sub-cellular bodies found in the cytoplasm of calls Eukaryotes are a group of organisms wit cells that have the genetic ‘material contained in a membrane-bound nucleus and also contain a number of membrane-bound erganelles such as mitochondria and chloroplasts, Prokaryotes are a group of organisms including bacteria and blue- ireen algae (cyanobacteria) that have few organelles and do not have the genetic material contained in a membrane-bound nucteus, ‘The cell surface membrane’ the membrane that forms the outer boundary ofthe eytoplasm of a call and controls the movement of substances into and out ofthe cell. Vesicles are membrane bags that hold secretions made in cel Polar lipids are lipids with one end attached toa polar group, eg. 1 phosphate group that makes one end of the molecule hydrophilic and one end hydrophobic. Gated channels are protein channels through the lip bilayer ofa ‘membrane that are opened or closed, depending on conditions in the cell The fluid mosaic model i the current model ofthe structure of the Cell membrane including floating proteins forming pores. channels and carir systems ina lipid bilayerEukaryotic cells 1 - common cellular uaa ico By the end of this section, you should be able to.. © describe eukaryotic cells, © describe the ultrastructure of eukaryotic cells and the functions of organelles including the nucleus, nucleolus, mitachondria, centrioles and vacuoles ning electron Most microscope images, apart rom those of living material or from ‘microscope, make cells appear flat and two-dimensional (2D). But cell a ‘asymmetrical three-cimensional (3D) shapes ~ so try to use your imagi look at cells and visualise them in three di The characteristics of eukaryotic cells In eukaryotie organisms such as animals, plants and fungi there is avery wide range of cifferent types of cel each with a diferent function, But thee are certain cel features that turn up agai and we can put these togetner as atypical plant or animal cell Remember that tis typical snot really exist, Dut acts asa useful guide to what to lock form any eukaryotic cell _-sytoplas cell surface membrane “4 Tom cell surface membrane | __smooth endoplasmic vacuole ‘jak Golgi body | |__ritochondrion rough ar envelope endoplasmic ff eticulum i ar pore [nucleolus tion ofthe electron microscope increaed our detaled knowledge and urctsand utre The typical animal cell Atypical animal cell contains many things that are common to all eukaryotic cells, including plants and fungi. Inside the cel surface membrane isa jelly-like liquid called the eytoplasm, containing @ nucleus ~ the two together are known as the protoplasm. The cytoplasm contains most of what is needed to carry out the day-to-day tasks of living, whilst the nucleus is vital to the long-term survival of the cell, because it contains the information needed to produce all the chemicals that make up ‘the cell This basie partern gives rise tan enormous number ‘of variations suited for the different functions that arise within the animal kingdom, The various parts of the cell have complex «and detailed structures, which we can see more clearly when ‘an electron microscope is used, The structures that can only be ‘observed in detail using the electron microscope are known as the ultrastructure of the cell, The structure of each part of the cell rates closely to the jab it has to do, Membranes Membranes in a cell are important both as an outer boundary to the cell and in the multitude of internal intracellular) ‘membranes In Seetion 2.1.2 you looked at the importance of cell membranes for controling the movement of substances, but membranes inside the cell also have other functions. They Jocalise enzymes in reaction pathways, for example respiration in mitochondria and photosynthesis in chloroplasts, and they ‘compartmentalise chemicals, for example hydrolytic enzymes in lysosomes. You will learn more about membrane functions ‘throughout this section as you consider the various structures that ‘make up the cell The protoplasm When the light microscope was the only too! biologists had to ‘observe cells, they thong thatthe cytoplasm was a relatively structureless, clear jelly. But the electron microscope revealed the cytoplasm to be fll of all manner of structures, known as organelles, some of which are described below. The nucleus ‘The nucleus is usualy the largest organelle in the cell (1-20 ym) and it can be seen with the light microscope. Electron micrographs show that the nucleus, which is usually spherical in shape, is surrounded by a double nuclear membrane containing holes or pores, known as the nuclear envelope. Chemicals can pass in and out of the nucleus through these pores. so that the nucleus can control events in the cytoplasm. Inside the nuclear envelope are two main substances, nucleic acids and proteins. The nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) (see Chapter 1.3). When the cell is not actively dividing, the DNA is bonded to the protein to form chromatin, which looks like tiny granules, Also in the nucleus there is at least one nucleolus ~ an extra-dense area of almost pure DNA and protein, The nucleolus is involved in the production of ribosomes. Recent research also suggests that the nucleolus plays a part in the control of cell geawth and division, Mitochondria ‘The name mitochondrion simply means ‘thread granule’ and describes the tiny rod-like structures that are 1 pm wide by up to 10pm long, seen in the cytoplasm of almost all eukaryotic cells Under the light micrascape. In recent years, by using the electran rmierascope we have been able to understand not only their complex structure, but also their vital functions. ‘The mitochondria are the ‘powerhouses’ of the cell, Here, in a series of complicated biochemical reactions, simple molecules are ovidised in the process of cellular respiration, producing ATP (see Chapter 1.3) that can be used to drive the other functions of ‘the cell and indeed the organism. The number of mitechondria [present can give you useful information about the functions ef a cell. Cells that require very little energy, for example white fat storage cells, have very few mitochondria, Any cell with an energy demanding function, for example muscle cells or cells that carry outa lot of active transport such as liver cells, will contain large rumbers of mitochondria. ‘An outer and inner membrane surround the mitochondria, They also contain their own genetic material, so that when a cell divides, the mitochondria replicate themselves under the control of the nucleus. This mitochonerial DNA is part of the whole ‘genome of the organism, Mitochonefia have an internal arrangement adapted for their function (see fig B). ‘The inner membrane is folded to form cristae, which give a very large surface area, surrounded by a fluid matrix. This siructure is closely integrated with the events in cellular respiration that take place in the mitochondrion (see Book 2 Sections 5.1.3 and 5.1.4). Backed by evidence that shows that mitochondria have their own DNA, scientists think that mitochondria and chloroplasts originated as symbiotic eubacteria living inside easly ces. Over millions of years of evolution they have become an integral part of the cell (see Section 3.1.5) ‘This is the endosymbiotic theory of the evolution of eukaryotic cells, cristae Inner mebrane “"] stalked particles matrix ‘outer membrane figB The 30 sc funcnons incl reof he ochondia (oe) scl 7The centrioles In each cal there is usually (Gee fg C). Bach centile is mad le and is about 0.5m long by 02 pm wide, The centrioles are nvlved in cel division, When cell divides, the centrioles pull apart to produce a spindle of microtubules that are involved in the movernent of the chromosomes, as you will se pair of centrioles near the nucleus chapter. (a) The cytoskeleton nown tata eytoskeleton i fils the cytoplasm (se fig D) Its made up of microfilaments, cshic are protein fibres, nd microtubules, sny protein tubes n diameter Microtubules are found both sin recent years H a feature of n. These micronubules cor lin, The cytoskeleton pi {in bundles throughout the cyt ly of the globular protein t several functions. It gives the cytoplasm structure and keeps the ‘organelles in place. Many of the proteins in the microfilaments are related to actin and myosin, the contractile proteins in mus and the cytoskeleton is closely linked with cell movement ‘and transport within cells. Recent research has shown that a ‘cytoskeleton is also a feature of some prokaryotic cells, rmicronubule ubulin sub-units angie tural and contractile te! Vacuoles ‘Vacuoles are not a permanent feature in animal cells These rane-lined enclosures are formed and lost as needed, Many ple anim around the prey they eng White blood cells in higher animals form similar v ‘engulfed pathogens, Contractile vacuoles are an important ‘in simple animals that live in fresh water be: tobe controlled. But in pite of these examples, vacuoles are not a major feature of make food vacuole jles aroundre Learning tips Remember that diferent types of electron microscopy provide very different types of information: + The scanning EM can show intact organelles allowing detailed measurements ofthe outer dimensions to be taken oritcan take 3D images along fracture lines «The transmission EM provides clear images ofthe internal structures of the organelles. “Together the information is useful to produce a detailed image ofthe ultrastructure ofa cel 1 Whatsthe role ofthe osteltn in he tops and why has its importance onl recently been recopised? 2. Explain the importance of onganelis in eukaryotic cals 3. Leokatthe dere images hat result rm rasan and seanrng electron mieoscpesin Chapter and ces ow they fer Sgges the avartages a enc ype o ae a ve evarpes where ach would be moreappropfte owe ‘Keydefinitions 0 ‘Cytoplasm i jlly-lke liquid that makes up the bulk of the call ané contains the organelles ‘The nucleus s an organelle containing the nucleic acids DNA (the genetic materia] and RNA, as well as protein, surrounded by a nuciear envelope with pores Protoplasm isthe cytoplasm and nucleus combined ‘The ultrastructure isthe detailed organisation ofthe cel, only visible using the electron microscope Intracellular means inside the cell (Chromatin isthe granular combination of DNA bonded to protein found inthe nucleus when the cells not actively dividing ‘Anucleolus is an extra dense area of almost pure DNA and protein found inthe nucleus involved in the production of ribosomes and control of growth and division Mitochondria are rod-like structures with inner and outer membranes that ae the site of acobie respiration Cristae are the infoldings of the inner membrane of the mitochondria which provide a large surface area. for the reactions of aerobic respiration, Eubacteria are true bacteria prokaryotic organisms). ‘The endosymbiotic theory isa theory that suggests that mitochondria and chloroplasts originated a= independent prokaryotic organisms that began living symbiotcally inside other cells as endosymbionts. Centrioles are bundles of tubules found near the nucleus and invalved in call division by the production (of a spindle of microtubules that move the chromosomes to the ends of the cell i the length ofthe cel, formed asthe A spindle is asetof overlapping protein microtubules runn centrioles pull apart in mitosis and meicss. ‘The cytoskeleton is a dynamic, 30 web-like structure made up of microfilaments and microtubules that fill the eytoplasm and gives it structure, keeping the organelles in place and enabling ell movements and transport within the cll Microfilaments are protein fibres that make up part ofthe structure of the cytoskeleton, Microtubules are tiny protein tubes about 20m in diameter that make up part ofthe structure ofthe cytoskeleton. vacuole is a fui-filled ca ty within the cytoplasm of a cll surrounded by a membrane. Contractile vacuoles ae vacuoles that can filland empty to help control the concentration ofthe {eytaplaem of simple freshwater animale 9Eukaryotic cells 2 - protein transport By the end of this section, you should be able to... © describe the ultrastructure of eukaryotic cells and the functions of organelles including the rough and smooth endoplasmic reticulum, 80 ribosomes, Golgi apparatus and lysosomes, ‘The cytoplasm of the cell contains the endoplasmic reticulum (ER), three-cimensional (3D) network of cavities bounded by membranes. The electron microscope reveals that some of the cavities are sac-ike and some are tubular. and that the ER spreads extensively through the cytoplasm. ‘The ER network links with the membrane around the nucleus, and makes up a lage part of the transport system within a cell as well as being the site of synthesis of many important chemicals. Ithas been calculated that 1 cm: of liver tissue contains about 11 m# of endoplasmic reticulum, Electron microscopes also helped scientists 1o work out the functions of the endoplasmic reticulum, by showing up the different forms - the rough and the smooth endoplasmic reticulum, Another useful technique isto provide cells with radioactively labelled chemicals that are building blocks for specific modules, for example labelled amino acids for the synthesis of proteins, and then find out where they appear in the cel. The labelled products can be tracked using microscopy ‘Anolhier method of locating them is to break the cells open and then spin the contents in a centrifuge. The different parts of the cell can be separated out and the regions containing the radioactively labelled substances identified. 80S and 70S ribosomes In Section 1.3.5 you met ribosomes, the organelles on which protein synthesis takes place in the cytoplasm of the cell. Ribosomes are made from ribosomal RNA and protein, and consist of a lenge subunit and a small subunit. The main type of ribosomes in eukaryotic cells are 80S ribosomes. ‘The'S' stands for Svedberg, a unit used to measure how quickly particles settle in @ centrifuge, The rate of sedimentation depends on the size and shape of the particle. When 80S ribosomes are broken into their evo units, they are made up of a 40S small subunit and a 60S large subunit. The ratio of RNA:protein in 808 ribosomes is 11 However eukaryote cells also contain another type of ribosome. Scientists have discovered 708, ribosomes in the mitochondria, and inthe chloroplasts of plant cells. These ribosomes are usually found in prokaryotic cells (bacteria and cyanobacteria), They are made up of a small 30S subunit and a larger 50S subunit and the ratio of RNA: protein in 708 ribosomes is 2:1 ‘These 70S ribosomes are reproduced in the mitochondria and chloroplasts independently when a cell divides. This is seen as good evidence for the endosymibiotic theory that mitochondria and Chloroplasts evolved from bacteria caught inside eukaryotic cells very early on in the process of evolution. Rough and smooth endoplasmic reticulum Electron micrographs show that much of the outside of the endoplasmic reticulum membrane is covered with granules, which are BOS ribosomes, so this is known as rough endoplasmic reticulum (RER) (sce fig A). The function ofthe ribosomes isto make proteins and the RER isolates and transports these proteins once they have been made. Some proteins, such as digestive enzymes {and hormones are not used inside the cel that makes them. so they have to be secreted without interfering with the cells activites. Ths is an example of exocytosis, ‘Many other proteins are needed within the cell The RER has a large surface aea forthe synthesis of all these proteins, and it stores and transpor's them both within the cell and from the inside to the Outside. Cells that secrete materials such a5 those producing the digestive enzymes in the lining of the gut, have a large amount of RER 80re Not all endoplasmic reticulum is covered in ribosomes (sce fig A). ‘Smooth endoplasmic reticulum (SER) is aso involved in symihesis and transport but inthis case of steroids and lipids. For example, lots of SERis foundin the testes, which make the steroid hormone testosterone, and inthe liver which metabolises chholesterel amongst other lipids. The amount and type of endoplasmic reticulum ina cell give an idea ofthe typeof job the cell does rough ER smooth ER fig A Rough and emooth endoplasmic resculun, Smooth Eis ore tbl than rough ERand alo lacks ribosomes onthe surface The Golgi apparatus Under the light microscope the Golgi apparatus looks like @ rather dense area of cytoplasm, Anelactron microscope reveals that its made up of stacks of parallel, attened membrane pockets alles cstemae formed by vesicles fom the endoplasmic Fetculunfosngtogeter coe Section 2.1.2, ig A). ‘The Golgi apparatus has a close link with, but isnot joined to, the RER. It has taken scientists along time to discover exactly ‘what the Golgi apparatus does. Materials have been radioactively labelled and tracked through the cell to try and find out exactly ‘what goes on inside it, Proteins are brought to the Golgi apparatus In vesicles that have pinched off from the RER where they were made, The vesicles fuse with the membrane sacs of the Golgi apparatus and the protein enters the Golgi stacks. As the proteins travel through the Golgi apparatus they are modified in various ways. Carbohydrate is added to some proteins to form glycoproteins ‘such as mucus. The Golgi apparatus also seems to be involved in producing materials for plant and fungal cell walls and insect culicles. Some proteins in the Golgi apparatus are digestive enzymes, These may be enclosed in vesicles to form an organelle known as a lysosome. Alternatively, enzymes may be transported ‘through the Golgi apparatus and then in vesicles to the cell surface ‘membrane where the vesices fuse with the membrane to release extracellular digestive enzymes. The Golgi apparatus was fist reported over 100 years ago, in April 1898, The flattened stack of membranes was observed by the Italian scientist Camillo Golgi (1843-1926) through alight microscope. For more than 50 years scientists argued over its function, Some thought it was an artefact from the process of fixing and staining during tisave preparation, ‘The arrival of the electron microscope in the 1950s allowed the detailed structure of the Golgi apparatus to be seen, ‘The electron microscope has been central in showing details of the internal structure of the Golgi apparatus, In addition, a number of techniques have been developed that have allowed ‘more detailed understanding. The most important of these has been the process of labelling specific enzymes so they can be seen using the electron microscope. The inner areas of the Golgi apparatus, nearer tothe RER, have been shown ta be very rich in enzymes that modify proteins in various ways. Ths is where most enzymes or membrane proteins are converted into the finished ‘product. In contrast, in the outer regions of the Golgi apparatus ‘you find lots of finished protein products, but not many of the fenzymes that make them, The mavement af cell membrane [proteins through the Golgi apparatus is very complex. Areas of ‘the protein thar need to be on the outside of the cell membrane, such as receptor binding sites, are crientated by the Golgi apparatus so that when they arrive at the membrane they are inserted facing in the right direction. ‘ae ‘endoplasmic reticuluen ‘a pinch off the rough endoplasmic / reticulum and fuse to form flattened sacs the Golgi apparatus — stack of Hattened cisternae lined with smooth =. a ee vesicles contining 0,0" secretions are pinched of the Golgi apparatus vvesiles fuse with the cell surface ‘membrane and release the secretions ig B The Goig apparatus rakes pros fem the RER, assembles anc paciages them and then transports them to where they are needed Temay be the suracs cf the cell or Meret repions id Lysosomes Food taken into the cell of single-celled protoctists such as Amoeba must be broken doy into simple chemicals that can then be used COrganeles inthe cells oF your body that are worn out need 10 be destroyed. These jobs are the function of the lysosomes. The ‘word Isis, from which they get their name, means ‘breaking dev! lysosomes appear as dark, spherical bodies inthe cytoplasm of ‘most cells and they contain a powerful mix of digestive enzymes. ‘They frequently fuse with each other and with a membrane-bound 81‘vacuole containing either food or an obsolete organelle. Thetr enzymes then break down the contents into molecules that can ‘be reused, A lysosome may fuse with the outer cell membrane to release its enzymes outside the cell as extracellular enzymes, for example to de trey bacteria or in digestion Lysosomes can also self-destruct If an entire cell is wearing out, needs to be removed during development, has @ mutation or is under stress, ts ly to destroy the entire contents of the cell. This programmed, controlled cell death is known as apoptosis. osomies may rupture, releasing their enzymes fig Good miroscopic evcence their functions in the Did you know? Apoptosis and disease Apoptosis or programmed cell death is vital to the maintenance of a healthy body. Lysosomes rupture and their enaymes are released to killcells that are old and coming to the end of ther heathy life, or calls that need to be removed during development, for example the webbing that initially farms between the fingers and toes ofa fetus inthe uterus. yzacomes may also desty cells in which the DNA, replication ystems not functioning properly. Butif apoptosis stops working properly if too many cell are destroyed, or nat enough lysosomes cupture so that cel death no longer takes place - this can have serious consequences for your health. For example, cancer is often thought of asa disease of uncontrolled cell growth. But scientists are increasingly convinced that uncontrolled growth is not the whole star. Cancer cells also filo die by apoptosis. Asa result they propagate the genetic mutations that allow them to reproduce uncontrollably. Excessive apoptosis aso causes problems It leads to the damage seen in the heart after a hear attack, and i inked to the death ofT killer cells in HIV/AIDS, This is covered in more detail in Book 2. The excessive rupturing of lysosomes may also be involved inautoimmune diseases such as theumatoid arthits, when cartilage tissue in joints self-destruct, and possibly in ather conditions such as osteoporosis and retinitis pigmentosa 82 1 What type of questions would scientists have asked when they set futto Investigate the funetions ofthe endoplasmic reticulum, anc how might they have set about finding the answers? Describe the role of the RER and the Golgi body in the production of both intracellular and extracellular enzymes, and explain the importance of packaging products within a cel 3. Why is it important that apoptosis does not occur more or less than it should? Investigate examples of diseases that are caused atleast in partby apoptosis Key definitions 0 The endoplasmic reticulum isa 3D network of membrane-bound cavities in the eytoplasm that links tothe nuclear membrane and makes up a large part of the cellular transport system as wells playing an important role in the synthesis of many different chemicals 805 ribosomes are the main type of ribosome found in eukaryotic cells, consisting of ribosomal RNA and protein, made up ofa 60S and 405 subunit. They are the site of protein synthesis, 705 ribosomes are found in the mitochondria and chloroplasts of ‘eukaryotic ces and in prokaryotic organisms, Rough endoplasmic reticulum (RER) is endoplasmic reticulum that is covered in 806 rosames and which is involved inthe production and transport of proteins. Exocytosis is the energy requiring process by which a vesicle fuses withthe cell surface membrane so the contents are released to the butside ofthe cell ‘Smooth endoplasmic reticulum (SER) is a smooth tubular structure similar to RER, but without the ibosomes, which is involved in the synthesisand transport of steroids and lipids in the cell. The Golgi apparatus consists of stacks of membranes that modify proteins made elsewhere in the cell and package them into vesicles for transport, and alsa produce materials for plant cell walls and insect cuticles ‘lysosome isan organelle fll of digestive enzymes used to break down wom out ces or organelles, or digest food in simple ‘organisms. ‘Apoptosiss programmed cell death - the breakdown of worn out damaged or diseased cells by the lysosomes,Eukaryotic cells 3 - plant cell structures By the end of this section, you should be able to... (© describe the ultrastructure of the cell wall in eukaryotic cells and relate its structure to its functions Plants, like animals, are eukaryotes. A typical plant cell has many features in common with a typical ‘animal cell (see Sections 2.1.3 and 2.1.4). They have many membranes and contain cytoplasm and ‘a nucleus, Rough and smooth endoplasmic reticulum spread throughout the cytoplasm, along with ‘an active Golgi apparatus. Mitochondria produce ATR which is as vital to the working of the plant cell as itis to the animal cell. However, there are several quite fundamental differences between plant and animal cells, They contain several kinds of organelle that are not found in animal cells including permanent vacuoles and chloroplasts, numerous chloroplasts tonoplast (membrane around vacuole} starch grain -cell wall (cell surface membrane underneath wall) sap vacuole tonoplast mitochondrion chloroplast cell wall (vith cell surface membrane beneath) (b) an electron micrograph and drawing of a plant cell 6000 fig the ight mcroscope ayes us the major fests a plant cl: th elation microscope rue many more ct 83The plant cell wall Animal cells can be almost any shape. Plant cells tend to be more regular and uniform in their appearance This lrpely because cach co's hounded by a ell wall You can visuals a panc cll as a ely file baloon nie a shoe box. The cll wall shoebox) isan important feature that ives plants their strength and suppor. Ir is made up largely of insoluble cellos (ee Section 1.2.2). The Plant cell wallis usualy ey permeable to everything that is solved in water ~it Goes not act Bs a barir to subslances getting into the cel. However the cel wall ean bocome impregnated with Suberin in cork tsues, or with lignin fo produce wood, These compounes act the permenbiy of the cell wall 90 that water and dissolved substances cannot pass through it. fig These cellos micofibsare made up of thousands of cellos chains held ogether by hyrogen bonds Ther oerttion and pacing changes fom primary to secondary ell wal, aficing bath eit and svergth “The plant cell wall consists of several layers. The middle lamella i th frst layer to form when a plant cel divides into two new cells. Iris made largely of pectin, a polysaccharide that acts like glue ‘and holds the cell walls of neighbouring plant ces together Pectin has lots of negatively charged carboxyl (COOH) groups and these combine with positive calcium ions to form calcium pectate. ‘This binds tothe cellulose that forms on either side. The cellulose microfibrils and the matrix build up on either side of the middle lamella. To begin with, these walls are very flexible, withthe cellulose microfioisall orientated in a similar ciection. They are known as primary eell walls. As the plant ages, secondary thickening may take place. A secondary cell wall builds up, with the celulose ‘microfibrils laid densely at cifferent angles to each other This makes the composite material much ‘more ngid. Hemicelluloses harden it further In some plants, particularly woody perennials. lignin is then added to the cell wals to produce wood, which makes the structure even more rigid, Within the siructure of a plant there are many long cells with cellulose cell walls that have been heavily lignified ‘These are known as plant fibres and people use them in many different ways including clothing, building material, opes and paper Plasmodesmata In spite of being encased in cellulose cell walls, plant cells seem to be in close communication with each other Intercellular exchanges seem to take place through special cytoplasmic bridges between the cells known as plasmodesmata (see fig C). The plasmodesmata sppear to be produced as the cells divide — the two cells do not separate completely, and threads of cytoplasm remain between them ‘These threads pass through gaps in the neviy formed cell walls and signalling substances can pass from one cell to another through the cytoplasm. The interconnected cytoplasm of the cells is known as the symplast, Scientists are still working herd to discover exactly how plant cells communicate through plasmodesmata. One clear piece of evidence showing that these incercelular junctions are vital in the life of plants comes from work with plant grafts. If we graft a rose onto 2 hardy root stock. the graft tissue only starts healthy cell division and grovith once plasmodesmata bridges are established between the host tissue and the graft issue.re endoplasmic reticulum cell membrane nS 4 Noe Sw) a ek ae “The plasmodesmata are lined with cell membrane and molecules pass freely from cell to cell through these canals. fig Plasmodesmasa provide a route for communication benween pa sacl how tor. 1 What role do cell walls pla inthe tacture ofa plant, and how stheirstructure elated 0 their function? 2 How does the pant cell wall change asthe cll rows and develop, and how does his affect thecal? 3. explain why plasmodesmata ar an npertan feature of lance structure Keydefinitions ‘cell wall ia freely permeable wallaround plant cell, made mainly of cellulose. Suberin is a chemical that impregnates cellulose cell walls in cork tissues and makes them impermeable, Lignin isa chemical that impregnates cellulose cellwals in wood and makes it impermeable, ‘The middle lamella isthe first layer ofthe plant cll wall tobe formed when a plant cell divides, made ‘mainly of calcium pectate (pectin) that binds the layers of cellulose together Pectin isa polysaccharide that holds cell walls of neighbouring plant cells together and is part ofthe structure of the primacy cell wall. ‘The primary cell wall isthe first very flexible plant ell wall te form, with all the cellulase microfibrils orientated ina similar direction. ‘The secondary cell walls the older plant cell wall in which the cellulose microfibrils have built up at dliflerent angles to each other making the cll wall mote rg. Plant fibres are long cll with cellulose cell walls that have been heavily lignifid so they are rigid and very strong, Plasmiodesmata ae cytoplasmic bridges between plant ces that allow communication between the cells ‘The symplast isthe interconnected cytoplasm of plant cells, connected by plasmodesmata, 85Eukaryotic cells 4 - plant organelles By the end of this section, you should be able to.. © describe the ultrastructure of the chloroplast, vacuole and tonoplast in eukaryotic cells, and relate these structures to their functions Plant cells contain several kinds of onganelle that are not found in animal cells. These include permanent vacuoles and chloroplasts. Permanent vacuole ‘A vacuole is any fluid-filled space inside the cytoplasm surrounded by a membrane. Vacuoles occur quite frequently in animal cells, but they are only temporary, being formed and destroyed when needed, [n non-woody plant cells the vacuole is a permanent structure with an important role, ‘The vacuole can occupy up to 80% of the volume of a plant cell. Its surrounded by a specialised membrane called the tonoplast. The tonoplast has many different protein channels and carrier systems in it It controls the movements of substances into and out of the vacuole and so controls the water potential of the cell. The vacuole is filled with cell sap, a solution of various substances, in water This solution causes water to move into the eell by osmesis (sce Section 4.1.3), and as a result the eytoplasm is kept pressed against the cell wall. Ths in turn keeps the cells turgid (swollen) and the whole plant upright. The pressures that can be developed in this way are very high indeed, ‘The pressure in leaf cell can be up to 1500 kPa ~ in contrast, the pressure in a human artery when the heart is pumping blood out into the body is only 16 kPa. As well as fulfilling the important role of maintaining the plant cell shape, the many different types Cf vacuoles in plants carry out a range of different functions. Vacuoles are used for the storage of a ‘number of different substances. Many vacuoles store pigments; for example the betacyanin pigment Of beetroot is normally stored in the vacuoles of the cells and does not leak out into the cytoplasm unless the root is cut, Ifthe tissue is heated, the characteristics of the membrane around the vacuole will change and so pigment wil leak out more rapidly. Vacuoles can store proteins inthe cells of seeds and fruits, and in some plant cells they contain lytic enzymes and have a function rather like lysosomes in animal cells. Vacuoles often store waste products and other chemicals. For example, digitalis, a chemical found in foxgloves that can act both as a heart drug and a deadly poison. is stored in the vacuoles of the cells. tonoplast, permanent vacole fg A The tonopias and the permanent vacuoles are key srucures nthe support systems of pants, but they have mary other functions as wal 86re Chloroplasts Of all ihe ferences berween plant and animal ells the prosence of ehloroplasts in plant cols probably the most Important because they enable plans to make thet own food. Notall plant ells contain chioropass~ only these cel fom the seen parts ofthe plant. However almost al plant cells contain the genetic information to make chloroplast and son some Ccreumstances diferent areas of a plant wil become green and Start to photooynihesise. The exceptions are parastc plants such as broomrape. Cells in flowers, seeds and roots contain no chloroplasts and neither do the internal cells of stems or the transport tissues In fact the majority of plant cells do not have chloroplasts, ut these organelles are very special and unique to plants, outer membrane inner mernbrane ‘There are some clear similarities between chloroplasts and ‘mitochondria Like mitochondria, chloroplasts + are large organelles: they have a biconvex shape with a diameter of 4-10 pm and are 2-3 ym thick + contain their own DNA, + are surrounded by an outer membrane + have an enormously folded inner membrane that gives a greatly increased surface area on which enzyme-controlled reactions, take place + are thought to have been free-living prokaryotic organisms that were engulfed by and became part of other cells at least 2000 millon years ago, However, there are also some clear differences, Chloroplasts + are the site of photosynthesis + contain chlorophyll, the green pigment that is largely responsible for trapping the energy from light. making it available fr the plant to use + are formed from a type of relatively unspecialised plant organelle known as a leucoplast. Amyloplasts Amyloplasts are another specialised plant organelle and, ike chloroplasts, they develop from leucoplasts They are colourless and store starch (see Section 1.2.2) This can then be converted to glucose and used to provide energy wien the cell needs it Amyloplasts are found in large numbers in areas of a plant that store starch, for example potato tubers. 1 Amoplass and chlorepass come om the same ype of Unpaid cll How do the wo stucutes ie? 2 Compare and contrast the structure of atypical plant cell with the structure of atypical animal cl, 3 Explain why chloroplasts are found only in particular parts of a plant. Suggest what happens to make part ofa plant, eg. a potato tuber, turn green when exposed to light? Key definitions ‘The tonoplast isthe specialised membrane that surrounds the permanent vacuole in plant cells and controls movements of substances into and aut ofthe cell sap. Cell sap is the aqueous solution tha fils the permanent vacuole. Osmosis isa specialized form of diffusion that involves the movement of solvent molecules down a concentration gradient through a patially permeable membrane, A chloroplast isan organelle adapted to carry cut photosynthesis, containing the green pigment chlorophyll. chlorophylls the green pigment hats largely responsible for trapping the energy from light, making it availabe for the plant 10 use in photosynthesis. ‘Amyloplasts are plant organelles that store starch 87By the end of this section, you should be able to.. Explain how. in complex organisms, cells are organised into tissues, organs and organ systems Multicellular organisms are made up of specialised cells but these cells do not operate on their own, The specialised cells are organised into groups of cells known as tissues. These tissues consist of one or more types of cells all carrying out a particular funetion in the body. However, tisaues do not operate in isolation Many tissues are further organised into organs, Tissues are groups of similar cells that all develop from the same kind of cel. Although there are many different types of specialised cells, there are only four main tissue types in the human body ~ epithelial tissue, connective tissue, muscle tissue and nervous tissue, Modified versions of these tissue types containing different specialised cells carry out all the functions of the body Fig A shows some different epithelial tissues, which hat form the lining of surfaces both inside and o of the body. Although some epithelial issues consist of more than one kind of cell, they all rest upon an extracellular basement membrane. Cells in epithelial tissues usually sit tightiy together and form a smooth surface that protects the cells and tissues are tissue: below Squamous epithelium is commonly found lining the surfaces of blood vessels, and forms the walls of capillaries and the lining of the alveoli. Cuboidal and columnar cells line many other tubes in the bod: Ciliated epithelia oiten contain goblet cells that produce mucus, These epithelia form the surfaces of tubes in the gas ‘exchange system and the oviduets. The regular waving of the cilia from side to side moves materials along inside the tubes. Compound epithelia are found where the surface is continually scratched and abraded, such as the skin. The thickness of the sue protects what lies beneath as new cells continue to grow. ‘muscle sue (0) brain tsus'(c) carage sue There are many other tissues in the body, including muscle tissue, nervous tissue, the collagen tissue and elastin tissue found in artery walls and the glandular tissue that secretes substances from inside the cells, Connective tissue is the main supporting tissue in the body, and includes bone tissue and cartilage tissue as well fas packing tissue that supports and protects some of the organs ‘Some of these tissues are shown in fig B. = ara 0} 001 oo] columnar basernent membrane Jolo {oolo 0} wo secreted \dloho\do|of— err xt ‘slondular ivision of cells of 3a { germinal layer pushes compound stratified fg There ore many binds of epitheliaOrgans ‘An organ is a structure made up of several different tissues that ‘work effectively together to carry out a particular function, There ‘are many organs in che human body, some of which are shown in fig C. Plants also have cells grouped into tissues and organs. For ‘example the leaf is an organ that is composed of vascular tissue, epithelial tissue and mesophyll tissues as shown in fig D. lungs liver intestine small intestine fig ¢ Someotthe organsas spongy mesophyll re Systems Innimals, in many cases a number of organs work together as an organ system to carry out large-scale functions in the body For txample the gestive system incudes the omans of the stomach, pancreas small and large intestines, and the nervous system includes the brain spinal cord and al peripherl nerves Most othe ells in tissue, organs and systems have dfereniated dung development so that they are capable of carrying oat the specific function. You wil ind out more about how this process happens in Book 2 Chapter 7.2 1 pin how the suucture of teflon sues related to thei fancion (2) squamous eptelum ning an sheoks (W iated eptheum ning a bronchus (0) muscle tisuein the bceps muscle 2 a) Choose one of the systems in the human body and describe brely the cells tissues and organs found within that system. (6) plain why this grouping enables the systom to caery ot its function effectively Atissue isa group of specialised cells carrying out a particular funetion in the body ‘An organ isa structure made up of several different types of issues grouped together to cary out a particular function in the body. Epithelial tissues are tissues that form the lining of surfaces inside and outside the body. [An organ system is a group of organs working together to carry out particular functions in the body upper epidermis palisade mesophyll xylem vessel phloem tissue 89,1 The photograph below shows a mitochondrion 3 (a) Draw and label a diagram to show the structure of as seen using an electron microscope, chloroplast, as seen using an electron microscope. [4]. (0) The photograph belaw shows a group of mitochondeia ina liver cell, as seen using an electron microscope. The ‘magnification is *50 000. (b) Make an accurate drawing of this mitochondrion enlarged 2. On your drawing label the matrix anda crista. [4] (Total: 6] ‘The phoragraph below shows a chloroplast as seen using an electron microscope, : Be () Messed ngthof the mactenon abled A mnlochondion jn Show ourverkage [S {ii) Name one other structure that might be visible in the ao “1 piareerespe inteteraencartis labelled A. u) (2) Name the parts labelled A and B. ial [Total: 9] (b) The actual length of the chloroplast berween X and ¥ is Sum, Calculate the magnification of this chloroplast. Show your working. (3 (c) Name one type of cell that contains chloroplasts. [1] (Total: 6]4. The table below refers to some cell structures. Complete the ‘ableby inserting the correct word, words or diagram in the appropriate boxes. Leave the shaded grey bexes empty ‘Name of cell structure Description of cell | Diagram of cell structure structure 1 Darkly-stained region in the nucleus 2. Where ribosomal [y)|__RNAis made Centrioles (2) lysosome [2 (2) T Hollow cylinders made of protein, 2. Form spindle fibres. el (Total: 6] 5 The photograph below shows some onion cells as seen using the high power of a light microscope. (a) Make an accurate drawing, enlarged »2, of the cell labelled A, Do not label your drawing, 8) 7 (0) Allthe onion cells have a cell surface (plasma) membrane. ‘The diagram below shows the structure of this membrane. coi heed so NOY SE BLE naam" Explain how the properties of phospholipids result in the formation of a bilayer proteins 81 [Total: 6] “The endosymbiotic theory received fresh impetus from a 1967 paper by Lynne Margulis, who offered evidence from microbiology. (2) What isa symbiotic relationship? (6) What do chloroplasts and mitochondria have in common with prokaryotic organisms? (c) Both chloroplasts and mitochondria have double membranes. When a white blood cell engulfs bacteria itforms a vacuole around them, Describe how this adds support to the endosymbiotic theory. (4) Further work by Lynn Margulis in 1981 argued that ceakaryotic fiagella came from bacteria called spirochaetes Explain why this has not received much support. ty) (Total: 4] () (1) (1) Scientists using light microscopes were unable to distinguish smal] organelles like ribosomes, (a) Name three other organelles that were too small for these scientists to see, i (o) Name two organelles that would have been seen using the light microscope. fa (c) Light microscopes can be used to watch substances move in realtime. Explain why this is impossible in an electron microscope. 1 [Total: 7] Cutline the stages of the production of the primary and secondary cell walls in @ perennial plant. (6) (Total: 6]TOPIC 2 Cells and viruses 2D) Beeler ere | Introduction “The human body c han it does human I the maths you need propriate uni— ' a yi} NY a eee eer ee, creme ee eh rene ae nea eerie err " pc areerag ee i ar ey Hole ee Bee fanaa Een een ae areoe| ieee ek ae Tce eae aan aS (oe eed VCC eee ef ee aii eo OO E. De uy at have | s Pur esperar ee eet ee es ee a erie ee eens ee eerie ri) protoctiss) vy PT esetTe his c eee eget cee es Cet coer et Pee ee ee ee per eae ees Se een erate cos pean eke eee eee ee ea er een eee errs See eee etd eee em td oer) Sead Some of the ethical implications of using untested Eevee aProkaryotic cells By the end of this section, you should be able to.. © describe the ultrastructure of prokaryotic cells and their organelles including nucleoid, plasmids, 70S ribosomes and the cell wall @ distinguish between Gram-positive and Gram-negative bacterial cell walls and explain why ‘each type responds dferently to some antibiotics Bacteria, cyanobacteria and archaebacteria are prokaryotic organisms, Bacteria alone are probably the most common form, of life on Earth, Some bacteria are pathogens and cause disease, but the great majority do no harm and many are beneficial to living organisms, for example as gut bacteria and inthe cycling of nutrients in the natural worlé, (see Book 2 Chapter 10.2) In this section, you will mainly consider the structure and functions of bacterial cells. mesosome? coll surface membrane alycogen granules Iipic droplets, 708 sbosomes cell wall plasmids* capfule or photagyntetic tucleid~ a long, circular slime layer membranes* strand of DNA 10 present in all bacteria fig Sucre of atypical bacterium The structure of bacteria ‘All bactetial cells have certain features in common, although these vary greatly between species, Bacterial cell walls All bacterial cells have a cell wall. The contents of bacterial cells are usually hypertonic to the medium around them, so water tends to move into the cells by osmosis. The cell wall prevents the coll swelling and bursting, Ic also maintains the shape of the ‘bacterium, and gives support and protection to the contents of the cell. All bacterial cell walls consist of a layer of peptidoglycan that is made up of many parallel polysaccharide chains with short peptide cross linkages forming an enormous molecule with @ net-lke structure. Some bacteria have a capsule (or slime layer if itis very thin and diffuse) around theit cell walls. This may be formed from starch, gelatin, protein or glycolipid, and protects the ‘bacterium from phagocytosis by white blood cells. Ir also cavers the cell markers on the cell membrane that identify the cell. Soa capsule can make it easier for a bacterium to be pathogenic (to cause disease) because itis not so easily identified by the immune 94 system. This is the case forthe bacteria that ceuse pneumonia, ‘meningitis tuberculosis (TB) and septicaemia, However, many capsulated bacteria do not cause disease. It seers likely that capsules evolved to help the bacteria survive very dry conditions ji and flagellae ‘Some bacteria have from one to several hundred thread-like protein projections fom their surface. These are called the pill (or fimbriae) and they are found on some well-known bacteria such as Escherichia col (E. ct) and Saimonella spp. They seem to be used for artachment to a hast cell and for sexual reproduction. However, they also make bacteria more vulnerable to virus infections, as a bacteriophage can use pili as an entry pointto the call. ‘Some bacteria can move themselves using flagella, These are litle bigger than one of the microtubules contained in a eukaryotic fRagellum, and are made of a many-stranded helix of the protein fageliin. The flagellum moves the bacterium by rapid rotations ~ ‘about 100 revolutions per second. Cell surface membrane ‘The cell surface membrane in prokaryotes is similar in both structure and function to the membranes of eukaryotic cells, However bacteria have no mitochondria so the cell membrane is also the site of some af the respiratory enzymes, In some bacterial cells such as Racilus subtilis a common soll bacterium, the ‘membrane shows infoldings known as mesosomes. There i still some debate about their function. Some scientists think they may be an artefact from the process of preparing the cell for an electron micrograph, others believe they are associated with enzyme activity particularly during the separation of DNA and the formation of new ‘ross walls during replication, It appears that other infaldings of the bacterial cell surface membrane may be used for photosynthesis by some bacterial species, Plasmid ‘Some bacterial cells also contain one or more much smaller circles of DNA known as plasmids. A plasmid codes for 2 particular aspect ofthe bacterial phenotype in addition to the zgeneiic inforrnation in the nucleaid, for example the production of | a particular toxin or resistance to a particular antibiotic. Plasmids ‘can reproduce themselves independently of the nucleoid, They ccan be transferred from one bacterium to another in a form of sexual reproduction using the pilNucleoid ‘The genetic material of prokeryotic cells consists of a single length of DNA, often circular, which is. not contained in a membrane-bound nucleus. However. the DNA is folded and coiled to fit into the bacterium, The ares in the bacterial cell where this DNA tangle is found is known as the nucleoid. In aan E colibacterium it takes up about halt of the area of the bacterium, 70S ribosomes ‘The bacteria, cyanobacteria and archaebacteria have no membrane-bound organelles, but they do have ribosomes where they carry out protein synthesis. The ribosomes in bacterial cells are 70S, smaller than the 80S ribosomes in eukaryotes. They have two subunits. The smaller is 30S and the larger is 50S (see Section 2.1.4), They are involved in the synthesis of proteins ina similar way to ‘eukaryotic ribosomes. Gram staining and bacterial cell walls ‘Whilst all bacterial cell walls contain peptidoglycan, there are in fact two main types of bacterial cell fig The ruceicd area ‘wall, These can be distinguished by Gram staining. a staining technique developed by Christian bass ‘Gram (1853-1938) in 1884 and stil in use today, Iris valuable because different types of bacteria are ‘vulnerable to different types of antibiotics and one of the factors that affects their vuinerabiity is the type of cell wal. Before staining, bacteria are often colourless, The cell walls of Gram-positive bacteria (c.g ‘methicilin-resistamt Staphylococcus aureus, MRSA) have a thick layer of peptidoglycan containing chemicals such as teichoic acid within its netlike structure, The crystal violet/iodine complex in the Gram stain is trapped in the thick peptidoglycan layer and resists decolouring when the bacteria are dehydrated using alcohol, As a result it does not pick up the red safranin counterstain, leaving the positive purple/blue colour surface proteins MRSA (ii ad plasma) Ih ‘membrane proteins Gram-positive bacterial cell walls ‘outer membrane proteins lipopolysaccharides membrane TORAH inner membrane proteins Gram-negative bacterial cell walls fg ¢ The difference in he cel wall suture ef the bacteria esis in he differen eactons wih he Gram stain 95‘The cell walls of Gram-negative bacteria have a thin layer of peptidoglycan with no teichoic acid between two layers of membrane. The outer membrane is made up of lipopolysaccharides. ‘After the crystal violet/iodine complex is applied, the bacteria are dehydrated in ethanol. The lipopolysaccharide layer dissolves in the ethanol leaving the thin peptidoglycan layer exposed. ‘The crystal violet/iodine complex is washed out and the peptidoglycan takes up the red safranin ‘counterstain, so the cells appear red Antibiotics and bacterial cell walls [Antibiotics are drugs that are used against bacterial pathogens. There are a number of different rypes Of antibiotics, each working in cifferent ways. They may work by affecting the bacterial cel walls, the cell membranes, the genetic material, the enzymes or the ribosomes. Antibiotics usually target features of bacterial cells that difer from those of eukaryotic cells, inuding the bacterial cel walls and the 708 ribosomes. Different types of bacteria are sensitive to different types of antibiotics. Doctors need to know if a pathogenic bacterium is Gram-positive or Gram-negative as this will ailect the choice of antibiotic used to teat the disease. ‘To pinpoint the actions of an antibiotic, first think about the difference between human cells and bacterial cells, and then about the differences between Gram-positive and Gram-negative bacteta, Some antibiotics, such as beta-lactam antibiotics (penicillins and cephalosporins). inhibit the formation of the peptidoglycan layer of the bacterial cell wall. Asa result they are very effective against Gram-positive bacteria, as they have a thick peptidoglycan layer on the surface of the cell but less effective against Grarn-negative bacteria, as their peptidoglyean layer is hidden and les vital to the wall structure. They don't affect human cells as they don't have a pepridogycan cel wall at all Giycopeptide antibiotics, such as vancomycin, are lage polar molecules that cannot penetrate the ‘outer membrane layer of Gram-negative bacteria, However, they are very effective against Gram- positive bacteria, even ones that have developed resistance to many crher antibiotics Polypeptide antibiotics, such as polymixins, are rarely used as they can have serious side effects ‘They are very effective against Gram-negative bacteria because they interact withthe phospholipids of the outer membrane. They do not affect Gram-positive bacteria Most other antibiotics affect both Gram-positive and Gram-negative bacteria because they target common processes such as protein synthesis by the ribosomes, They only target prokaryote ribosomes, not eukaryotic ones, If you are studying A level Biology. you will learn more about antibiotics in Book 2 Gram staining © positive negative 3 38 Minimum inhibitory concentration (ygem”?) on oot 001 Penicilin Neomycin Streptomycin Antibiotic fig This graph shows that penclin i effective ageine Gram postive bacteaa¢ all the Blue cies are on below bgem, so all ypes of Gram-posiive bactsria are ile at relat ely lows dose, Neomycin is best for Gram negative bacteria as al thered ices ate below 2 gc Septomycin is he abe to choose ithe Gam ‘staus of the bactera is unknown ecause kills all 'ypes of bacteria ata dose of only 14 gem 96er Alternative ways of classifying bacteria Grouping bacteria simply by the way their cell walls do or do not take up Gram stains is of limited use in classifying the different types. Another way in which bacteria can be identified is by their shape. Some bacteria are spherical (cocei) while che baeilli are rod-shaped. Yer others are twisted (spirilla) or comma-shaped (vibrios). Bacteria are also sometimes grouped by their respiratory requirements. Obligate aerobes need oxygen for respiration, Facultative anaerobes use oxygen if itis available, but can manage without st, Many human pathogens fll into this group. Obligate anaerobes can only respire in the abs cof oxygen ~ in fact oxygen will kill them. 1 Make tube to compar and contrast protarticand eukaryotic el N ‘What is the difference inthe structure of the walls of Gram-positive and Gram-negative bacteria? w (@) How does the structure of the walls of Gram: positive and Gram-negative bacteria affect the effectiveness of some antibiotics? (©) Using the data in fig D suggest why streptomycin would be the best of these three antibiotics to use if ‘you did not know whether a bacterial pathogen was Gram-positive or Gram-negative ‘Keydefinitions ‘hypertonic solution isa solution with a higher concentation of solutes and lower concentration of \water (Solvent than the surrounding solution. Peptidaglycan isa large, net-like molecule found in all bacterial cell walls made up of many parallel polysaccharide chains with short peptide cross-inkages. imbriae) ar thread-lke protein projections found on the surface of some bactria, Bacteriophages are viruses that atack bacteria Flagella are many-stranded helices of the contractile protein flagellin found on some bacteria, They move the bacteria by rapid rotations Mesosomes are infoldings of the cell membrane of bacteria. ‘Anucleoid isthearea in a bacterium where we find the single length of coiled DNA. Plasmids are small, circular pieces of DNA that code for specific aspects of the bacterial phenotype. {Gram staining is a saning technique used to distinguish types of bacteria by their cll wall Gram-positive bacteria are bacteria that cantain teicholc acid in their cell walls and stain purple/blue with Gram staining, ‘Teichoic acid isa chemical found in the cell walls of Gram-positive bacteria. ‘Gram-negative bacteria are bacteria that have no teichoic acd in ther call walls. They stain red with Gram staining, Cocei are spherical bacteria, Bacill ae rod-shaped bacteria, Spirilla are bacteria with a twisted or spiral shape. Vibtios are comma-shaped bacteria. (Obligate aerobes are organisms that need oxygen for respiration, Facultative anaerobes are organisms that use oxygen fit is available, ut can respire and survive without it Obligate anaerobes are organisms that can only cespire inthe absence of oxygen and ar killed by ‘onygen. 7Mtg -13 By the end of this section, you should be able to.. © recognise that viruses are not living cells © explain the classification of viruses based on structure and nucleic acid types as illustrated by A (lambda) phage (DNA), tobacco mosaic virus and Ebola (RNA) and human immunodeficiency vius (RNA retrovirus) © describe the lytic cycle ofa virus and explain latency Viruses are the smallest of all the microorganisms, and range in size from 0.02um to 0.3yum across, about 60 times smaller than the average bacterium, Viruses are not cells. They are arrangements of genetic material and protein that invade other living cells and take over their biochemistry to make more viruses It is because of this reproduction and the fact that they change and evolve in an adaptive way, that they are classed as living organisms. Viruses “Most scientists working on viruses class them as obligate jnracellular parasites, meaning they can only exist and reproduce as parasites in the cells of other living organisms Because natural viruses invade and take over ving cells to reproduce, they usually all cause damage and disease of some sort. They can withstand drying and long periods of storage whilst maintaining their ability 10 infect cells There are very few drugs that have any effect on viruses, and those chat do only work in very specific instances; for example, acyclovir can help prevent herpes (cold sores) and genital herpes. Did youknow? Discovering viruses People suspected the presence of viruses causing disease inthe late rineteenth century, They were developed as a model to explain the way certain diseases were passed from one individual to another, but twas not until 1935 thatthe first virus was identified by Wendell Stanley (1904-71), ‘The leaves of tobacco plants are prone to an unpleasant blotchy dlisease that has a devastating elfecton the plants, and no-one could Find the cause. Stanley pressed the juice from around 1300kg of diseased tobacco leaves. After extraction and purification, this produced pure, needle-like crystals which, if dissolved in water and painted onto tobacco leaves, caused the symptoms of the disease, The particies were called tobacco mosaic virus (TMV), [twas abvious thatthe erstals were no ving in the usual sense ofthe word, yet. they retained the ability to cause disease, Viruses cannot be seen Using a ight microscope because they are usually smale: than halla wavelength of light. With the development ofthe electron microscope the TMY particles were shown to be rod-like structures, with a protein coat formed around a core of RNA. 98 fig. The tiny roc shaped paricles ofthe tobacco mesaic virus seen here under thescanning decron merozcope, can cause setious damage to a Cop The structure of viruses Viruses usually have geometric shapes and similar basic structures, However there is considerable variation inthe genetic material they possess, the structure of their protein coat and whether or not they have an envelope. The protein coat or capsid is made up of simple repeating protein units known as capsomeres, arranged in diferent ‘ways, Using repeating units minimises the amount of genetic ‘material needed to code for coat production. It also makes sure that assembling the protein coat in the host cell is as simple as possible, In some viruses the genetic material and protein coat is covered by alipid envelope, produced from the host cell. The presence of the ‘envelope makes it easier for the viruses to pass from cell to cel, ut it does make them vulnerable to substances such as ether, which will ssolve the lipid membrane. Classifying viruses Viruses attach o their host cells by means of speci proteins {antgens)inown 25 virus attachment particles (VAPS) hat target proteins in the hos cel surface membrane Because they respond to partclar molecales ofthe host cell surface viruses are Giten gute spect inthe issue they atace Viruses are classified by their genome and their mode of replication, Viral genetic material can be DNA or RNA, and the nucleic acid is sometimes double-stranded and sometimes single. The way in which the viral genetic material is used in the host cell to make new viruses ‘depends on which form itis in + DNA viruses: In these viruses the genetic material is DNA. The viral DNA acts directly as a template for both nev viral DNA. and forthe mRNAs needed to induce synthesis of viral proteins. ‘Examples of DNA viruses include the smallox virus, adenoviruses, ‘hich cause colds, and some bacteriophages (viruses which infect bacteria) for example the 4 (ambda) phage in fig B + RNA viruses: 70% of viruses have RNA as their genetic ‘material and they are much more likely to mutate than DNA, viruses. RNA viruses do not produce DNA as part of ther fe cycle. The majority of RNA viruses contain a single strand of RNA and are know as ssRNA viruses, Positive ssRNA viruses (also known as positive-sense ssRNA viruses) have RNA thatcapsomere — repeating protein unit ‘hat makes up the protein coat (@) capsid ~ protein coat nucleic acid ~ genetic ‘material that may be double or single Stranded, DNA or RNA receptors Viral proteins often involved ‘envelope lipid derived inattachment io host cell from host cell membranes = not always present can act directly as mRNA and be translated atthe ribosomes. Examples of plant and animal diseases caused by positive ssRNA viruses include tobacco mosaic viruses, SARS, polio and hepatts C. Negative ssRNA viruses (also known as negatve-sense ssRNA vinuses) cannot be directly translated ‘The RNA strand must be transcribed before itis translated atthe ricosomes. Examples of diseases caused by negative ssRNA viruses include measles. influenza and Ebola + RNA retroviruses: Resrviruses area special ype of RNA virus, They have a protein capsid and a lipid envelope. The single strand of vitel RNA directs the synthesis ofa special ‘enzyme called reverse transcriptase. This goes on to make DNA molecules corresponding tothe vial genome. This DNA is, then incorporated into the host cell DNA and used as a termplate for new vial proteins and ukimately @ new viral RNA genome. HIV (human immunodeficiency virus is a retrovirus and some forms of leukaemia are also caused by thstype of virus. How viruses reproduce Natural viruses all cause diease. and they attack every ler known ype of living organism. There are even Vises that attack bacteria ‘known as bacteriophages. Weare constaniy involved in abate agnin the vines thar cause disease in curselees, cu animals, ur ‘rope and our ervronment. In Ger to understand how vases case damage tothe body. and tobe abe to try to target crags effectively it 'simportant to understand how they repredacein the human bod Virus life cycles’ Viruses only reproduce within the cells of the body: They attack their host cells in a number of diferent ways For example, bacteriophages inject their genome into the host cel, but the bulk Of the viral material remains outside the bacterium, The vital DNA forms. citce or plasmid within the bacterium. ‘The viruses that infect animals get into the cells in several ways. ‘Some types are taken into the cell by endocytosis — either with or ihout the envelope — and the hest cell then digests the capsid, releasing the viral genetic material. Most commoniy, the viral ‘envelope fuses with the host cel surface, releasing the rest of the B General viral stuctures (a) RNA wires, (b) (amb phage; c) elecron micrograph of A [ambsda)bacterioohages virus into the cell membrane, Plant viruses usually get into the plant cell using a vector, often an insect such as an aphid, to pierce the cell wall DNA virus replication nee a virus isin the host cell there are two different routes of infection: Latency - the lysogenic pathway Many DNA viruses are non-virulent wien they fist get into the host cell They insert their DNA ina the host DNA so iis replicated everytime the host cell divides, This DNA inserted into the hosts called « provirus, Messenger RNA is not produced fom the viral DNA because one of the viral genes causes the production ofa repressor protein that makes it impossible to translate the ret of the viel genetic material The virus does not affect the host cell or make the host organism ill at this stage in the life cyele. Duting this period of lysogeny, when the virus is part of the reproducing hest cel, the virus is said to be latent. The lytic pathway Sometimes the viral genetic material is replicated independently of| ‘the host DNA straight after entering the host. Mature viruses are ‘made and eventually the host cell busts leasing large numbers cf new virus particles to invade other cells The virus said to be virulent (disease causing) and the process of replicating and Ieling cells is knawm as the ytic pathway Under certain conditions, such as when the host is damaged, viruses in the lysogenic state are activated. The amount of repressor protein decreases and the viruses enter the lytic palhway and become virulent (see fig C), Some types of virus have both latent and lytic stages in their life cycle, but others move straight to the iytic stage after they have infected a cell RNA virus replication ‘There area number of different types of RNA viruses and they replicate themselves indifferent ways 99)1 ‘T2 bacteriophage attaches to bacterium. 2 Phage DNA is injected into host cell. Itbrings about the synthesis, of viral enzymes. or - ca 9 = Lysis — the bacterial cell bursts due to the action of lysozyme, releasing up to 1000 phages to infect other bacteria 3a » New phage parties are assembled Virel DNAs Phage DNA J) os new protein coats are made sround into host the host DNA, Fyiesied or released cell DNA. and takes over the cell rm siutpnia y besten | replicated each time the - bacterium divides, changes to ~ aa be without causing jin lytic Phage DNA ‘any damage. pathway is replicated. gC The ife cycle ofthe T2 bacteriophage includesa latent, Wsogenic phase and ay phase Positive ssRNA viruses ‘These are viruses that contain a single strand of RNA that is a sense strand. Its used directly as mRNA for translation into proteins atthe ribosomes ‘The proteins made include viral structural proteins and an RNA polymerase, which is used to replicate the viral RNA. Negative ssRNA viruses ‘The single strand of RNA in these viruses is an antisense strand, Before it can be used to make viral proteins and more viral RNA it must be transcribed into a sense strand. The virus imports, RNA replicase, which uses free bases in the host cel to transcribe the antisense RNA strand and produce @ sense strand that can be translated atthe ribasomes, Once the RNA strand has been transeribed it acts as mRNA at the ribosomes and codes for Vira proteins including RNA replicase. These viral proteins combine ‘with replicated viral RNA to form new viral paticles. RNA retroviruses Retroviruses, including the HIV virus that causes AIDS and the Rous sarcoma virus that causes cancer in chickens, have a rather different and complex life cycle. They have viral RNA as their ‘genetic material It cannot be used as mRNA, buts translated into DNA by the viral enzyme reverse transcriptase in the eytoplasm of the cell, This viral DNA passes into the nucleus of the host cell ‘where its inserted into the host DNA. Host transcriptase enzymes ‘then make viral mRNA and new viral genome RNA. New viral 100 ‘materia is synthesised and the new viral particles leave the cell by exocytosis (see Section 2.1.4). The host cell continues to function as a virus-making factory, while the new viruses move on to infect other cells, poave strand >| proteins ==> mae RNA earscpion | poses rand Sn AAs aetna ee crandlaton ‘ 5 cco viruses [7] proteins fig Repiczion ofa negntve RNAVINSee 1 o-—retrovirus (HIV) ‘The retrovirus attacks an 3 Viral RNA is translated into viral DNA by reverse transcriptase in the cytoplasm. viral transcriptase viral DNA, 4 Viral DNA is incorporated into the host DNA jin the nuclecs, Iedirects the production of new viral genome RNA, mRNA 5 ng *@ e.”. fig Thelife cle ofa reovins act as a virus factory Viruses and disease Viruses cause disease in animals, plants and even in bacteria, ‘They can cause the symptoms of disease by the lysis of the host cells, by causing the host cells to release their own lysosomes (see Seetion 2.1.4) and digest themselves from the inside or by the production of toxins that inhiit cell metabolism. Viral infections are often specific to particular tissues For ‘example, adenaviruses, which cause colds affect the tissues of the respiratory tract, but do not damage the cells of the brain or the intestine, This specificity seems to be due to the presence or absence of cell markers on the surface of host cells Each type of cell has its ovm recognition markers and cifferent types of virus, can only bind to particular markers. The presence or absence of these markers can even affect whether a group of living ‘organisms is vulnerable to attack by viruses at al. For example, the angiosperms (flowering plants) are vulnerable to vial diseases, but ‘the gymnosperms (conifers and their relatives) are not Viruses are well-known for causing diseases like flu, measles, AIDS and s they play a role in the development of cancers. Certain animal cancers hhave been clearly linked to viral infection, and in humans there seems to be a link in certain specific cases. For example, the ‘human papilloma virus responsible for warts on the skin, including ‘genital warts, has been linked with the accurrence of pre cancerous and cancerous changes in the cells of the cervix, and ‘there is now a vaccine against it 1 what adaptations make viruses such sucessful pathogens? a. Research also shows that in some ca: 2 sugges vali argument forthe ase tha: (a) wrutesare hing organs (0) sass are not ving organisms 3 What are the main differences between the Iytic and lysogenic pathways of infection by DNA viruses? 4 Make table to compare the deren ways in which RNA vises reproduce Key defini ‘An envelopes coat around the outside ofa virus derived from lipids in the host cell. The capsid isthe protein coat ofa virus Capsomeres are the repeating protein units that make up the capsid ofa virus, Virus attachment particles (VAP) are specific proteins (antigens) that target proteins inthe host cell surface membrane. DNA viruses are composed of DNA asthe genetic material RNA viruses are composed of RNA as the genetic material. Retroviruses area special type of RNA virus that contol the production of DNA corresponding to the viral RNA and insert it into the host cell DNA Reverse transcriptase is an enzyme synthesised in the lifecycle of a retrovirus that makes DNA molecules corresponding tothe viral RNA genome, [Non-virulent is. term used ta describe a microorganism that is not disease-causing provirus isthe DNA thats inserted into the host cell during the lysogenic pathway of reproduction in viruses. Lysogeny is the period when a virus is part ofthe reproducing host cell, but does not affect it adversely. Latentis the state of the non-virulent vius within the host cel Virulent isa term used to deseribe a microorganism that i disease causing 101Controlling viral infections By the end of this section, you should be able to.. © Describe how antiviral medicines work by inhibiting viral replication because viruses are not living cells, (© Explain how control of viral infections focuses on the prevention of the spread of disease as vial infections are difficut to treat © Evaluate the ethical implications of using untested drugs during epidemics As you have seen, the lifecycle of a virus involves the destruction of host cells. As a result of this direct damage, and the response of the host body to infection, viruses usually cause disease in the ‘organisms they infect. The spread of viral diseases Viral diseases are spread in many diferent ways, The key featre isthat material carrying viuses from an infeted animal or plant comes ino contact vith vulnerble issues in snother uninfected crganis, So, viruses may be spread trough infected mucus Groplets of salva, infected blood or faeces or simple contact becween infected organisms. Intemational travel means that Ciseases that would once have use caused loca outbreaks can row rapidly spread all ve the word Diferent viral diseases are Spreadin deren ways, For example: > Footand.mouth disease is serious disease of coven hoofed animals such as cattle It severe weakens adult animals and Flsa high percentage of young animals tis spread through body secretions, suchas ik and semen, and tensed in the breath and the faeces of infected animals. Healthy animals Can pik up the virus om contaminated pera, ood, water, Contact with eseased animals and even om infected meat and primal procucs they are eaten, + Bhola isa severe viral ilness caused by the Ebola virus tis often fatal especialy ite symptoms ae untreated. lis an tnimaleigeae tht spread to humans through the faeces urine blood and meat of infected animals. then spreads easly fom person to person by the det contact of the sn ormmucous Iembranes of a heathy person with bloo, feces and other body secretions of an infected person, or even bedding and surfaces contaminated with fs fom an infected person Treating viral diseases ‘As you have seen, bacterial diseases can be treated with antibiotics. The drugs affect the bacterial celis in one way or another (see Seetion 2.2.1). Viruses, however, are not living cells inthe conventional sense. Scientists have not yet developed drugs that cnn affect the vnos particles themselves. Instead antiviral teatments target viru replication. There area numberof diferent ways in which they can work They can + target the receptos by which viruses recognise their host ells 102 + target the enzymes that help to translate or replicate the viral DNA or RNA. + inhibit the protease enzymes that enable new virus particles to bud from host membranes, So far, scientists have not been able to cure viral diseases, but they hhave reduced the time a person is sick (see fig A) and can delay the development of symptoms after infection (e.g the cocktail of antieuoviral drugs used to treat HIV/AIDS). In adult patients: 30% (32 hour) reduction in duration ofillness. S38 96 aan uc = o Placebo (n = 129) ‘Tamifiu™ treatment (n = 129) Preventing viral disease ‘Some viral diseases, such as the common cold, are relatively mild and have a very low mortality rate Others, however, are very serious. During 1918-19 an outbreak of influenza killed up co six times more people than the whole First World War. Foct-and- ‘mouth disease has an almost 100% mortality rate in young stock. Inthe 2001 UK epidemic of foot-and-mouth disease there was no ‘treatment avaliable and no tests to reliably identity infected animals before they showed symptoms $0 all of the cloven-hoofed animals Con infected farms were destroyed and burned to try and prevent the spread of the virus to other farms in the area, Over 6 milion animals were kiled, Veterinary scientists are working on developing sensitive tests to idenbiy infected animals so that control of the cisease may be possible in the future without this extensive culling, fig Mass culing and burning of posbly infected ivestock uring the 2001 cutbreak of fost and-meuth disease in te UK was eventually succes in stopping the spre ofthe deense ‘The mortality rate of humans infected with Ebola varies but can be very high with 25-90% of people infected withthe disease ‘ying, Mortality depends on the strain of the virus, the health of the infected person and the speed with which they get support and health care, The average mortality rate is around 50% Viral diseases like these can be devastating, Because there are no antiviral drugs against most viral infections, disease control focuses on vaccination and reducing the spread of virusesVaccinations ‘Vaccination plays a major role inthe prevention of disease ‘outbreaks. When you are vaccinated against a disease you become ‘immune to it and so will nt become infected should you encounter it Ideally everyone is vaccinated agains serious diseases that may feet ther. If an epidemic breaks out and the population is not ‘vaccinated, there is rush to deliver vaccines to everyone wiho is not already infected. Usually health care workers, the very young ‘and the elderly are vaccinated frst. Unfortunately we have not yet developed flly-tested vaccines against some of the worst vial diseases, such as HIV/AIDS and Ebola. You will learn more about ‘vaccination if you continue to study A level Biology Disease control Understanding the cause of a disease and how itis spread means ‘we can work to contal it. Disease control is particularly important ‘when an epidemic occurs. An epidemic is when the levels of people with a particular disease are much higher then expected ‘vera given period of time. When theres a vaccine available, this 's the time for mass vaccination of vuinerable people, alongside measures to prevent the spread of disease. In diseases where no vaccine is avaiable, controling the spread of the disease is key. Identijing the pathogen early and putting control measures in place can make all the difference to the numbers of people affected (see fig C) ‘Ongoing detection and response confirmation 100 response fst case e Cases detection ‘opportunity for control 30 ‘Time/days ‘Ongoing detection and response opportunity erection for control ‘confirmation 100 rst Cases of 20 Time/days 1¢ These raps show the dference that effecve detection and response 9 make to the numer ofcazee hat cevelop. er ‘There are a number of different ways of controlling the spread of a disease. Some are relevant to all diseases, some are only used in ‘more extreme diseases such as Boola, They include: + Rapid identification of disease: For example, in West Africa in 2014. it was some timne before the Ebola was recognised and ellective testing regimes putin place. If the disease is bacterial, it must be identified and an effective antibiotic used, + Nursing in isolation: This is used for serious infections such as Ebola and C. difficile only. Itis readily available in countries such as the UK but sealed isolation units are rarely available in developing countries such as those in West Africa, This lack of health infrastructure makes it difficult to isolate people affected by diseases such as Ebola. When il people are cared for within their families the virus spreads easily Simple units nursing all. infected patients together can help. + Preventing transmission from one individual to another: Simple measures such as reguiar hand washing, hand washing before and after every contact with patients by health workers and families, care in handling body fluids and wastes, careful disposal of infected bodily wastes, and frequent disinfecting of| surfaces and people are key. Body fluids are very infectious in Ehola cases and good hygiene is vital + Sterilising or disposing of equipment and bedding after use: (One of the main transmission routes for Ebola at the beginning, of the epidemic was through unsterlized needles used in an antenatal clini, + The wearing of protective clothing by health workers: When dealing with dangerous and highly infectious viruses such as hola, health workers should wear facemasks, gowns, gloves, and goggles to protect the eyes, The slightest contact of infected material withthe eyes is enough to lead to infection. “The gloves should be washed and cisinfected before removal and then the hands washed as well + Indentifying contacts: Feople who have been in contact with infected people need to be monitored so that they can be ‘weated and/or isolated rapidly if they show signs of disease Did youknow? Rituals and infection ‘Many cultures have rituals that are cartied out after a death, Family and friend may visit touch and kiss the body, and they may wash the body and prepare itfor burial in the family home, inthe case of a lisease such as Ebola, the body remains highly infectious ater death and so funeral ntuals ean lead to outbreaks of further infection, It was observed that about a week after the funeral af an Ebola victim, ‘many of the mourners would become sick themselves, Communities accepted that these rituals had to be changed to prevent the spread ‘of Ebola. y sealing bodies in plastic and burying them immediately ater death the spread of the disease was greatly reduced In the twenty-first century, in countries such as the UK, we expect, tobe able to take some medicine and get better if we feel unwel, In an epidemic caused by a virus this isnt always possible due to limited treatment options. If the epidemic is of a potential killer disease, such as flu or Ebola, the pressure to find an effective treatment or vaccine is very high. 103The development of new medicines ‘The development of a new medicine or vaccine takes up to 10 ‘years, involves many diferent scientists and doctors, and costs mmlions of pounds Initial ideas for potential drugs come fram a ‘wide range of sources including genome analysis of pathogens, computer modelling, clinical compound banks and medicinal plants. These chemicals have to go through thorough research and testing on cell and tissue cultures, safety analyses and molecular modifications. This is followed by animal testing to ensure the compound works in a whole organism and is safe. This is then followed by three phases of human testing to further ensure safety and thatthe drug works well. This goes along with complex regulation ang licensing procedures until finaly. new drug may reach the doctor’s surgery. This process is summarised in fg D. [ase] fig This diagram summarises the man stages inthe normal rug ‘evelopment process, Speeding up the process When an epidemic develops, sme ofthe fal tages of the testing of anew medicine or vaccine may be speeded up to try ani save Ives and prevent the spread of a deadly disease, Here are two examples Jn 2006 a new strain of HSNI fu (known as bird fu) caused a ‘global pandemic. A vaccine against the new strain was produced ‘very quickly fast-tracked using existing techniques and technology for proxiucing annual fl vaccines and put through basic clinical trials ‘They were to be used for health workers ifthe pandemic hit the UK. The Medical Research Council said they expected the ‘vaccines would give some, if not tora, protection whilst a better ‘vaccine was developed. In addition, antiviral medicines such as ‘Tamiful™ and Relenza™ were stockpiled in spite of concerns that there was incomplete data about their effectiveness. These concerns were raised again when the drugs were used in the 2009 swine flu epidemic and the Cochrane Collaboration, which carries, out systematic analysis of the published data on medicines, has since stated that these drugs have not been proven to reduce hospitalisations and serious complication from influenza. You will learn more about influenza in Book 2. ‘The first case of Ebola in this outbreak occurred in late 2013 in ‘West Africa. However it took until mid-2014 for the world beyond Affica to recognise the size and severity of the outbreak of disease 104 and the speed with which it was spreading, Once the severity of the ‘outbreak was recognised, the World Health Organisation (WHO) ‘and pharmaceatical companies around the world looked for ways to fast-track drugs and vaccines that were already in development and had passed many of the development stages, but which had not ‘completed human trials In this situation there are two challenges: to make sure the drugs are safe and effective and also to ramp up production tobe able to make enough of the medicine or vaccine frit to be useful, Potential treatments inchuded: + ZMapp"™, an experimental drug produced afterlongsterm stuies, (of people who had survived Ebola in previous lest-widespread outbreaks. Scientists had genetically modified tobacco plants to produce three antibodies that seem to be associated with surviving the disease In trials it was effective in treating monkeys, but had ‘ot been tried on people. Tiny amounts of the drug were available and used to reat 7 people including Aiean, American, Spanish {and British health workers who developed Ebola, Some recovered, ‘butsome of the seven died, as you would expect with a disease vith around 50% mortality. Scientists are trying to produce more of the substance to run bigger tras on more people. + Vaccines: Several companies had vaccines in trials that are ‘being fast-tracked for use against Hola. They are making many doses of the vaccine so that if they are safe to use in humans, ‘many health workers and then people living in epidemie areas can be vaccinated, Other pharmaceutical companies are supporting the work of| ‘companies with drugs and vaccines closest to completion, and are also developing other drugs against the vias itll Ethical implications Historically, doctors and scientists tried out new medicines on themselves, their families or their patients wit litle orno testing crtrals. Today it would be considered completely unethical under normal circumstances to give anyone a medicine or vaccine that had not been through the full process of testing and approval However in severe epidemics or pandemics, with thousands of lives at risk, decisions may be made to use drugs that are only part ‘way through the full testing process. Most often this involves drugs that have not completed human trials. Although the media will report these as ‘untested’ they have infact already undergone @ ‘minimum of five years testing and development, and often wil be part way though human trials “There are a number of factors that have to be evaluated when considering whether a drug should be fast-tracked for use in an epidemic. These include + the seventy of the disease + the availablity of any other treatments for the disease + the effectiveness of standard disease control measures in halting the spread of the disease + transpareney about the process and informed consent of those given the treatment + freedom of choice over participation + involvement of the affected community ~ community consent for treatment can be more valuable than individual consent+ collection of clear clinical data from the use of new medicines in this situation so an on-going assessment of the safety and ‘efficacy of the drug or vaccine can be made Reasons against using untested drugs include: + Some people simply feel that its not ethical under any Circumstances to use drugs that have not completed full human vials +f an untested drug produces unexpected side effects it ean ‘make the situation worse + Deciding who gets the drug or vaccine can be difficult. For, ‘example, ina situation such as the Ebola epidemic, local people might fee! they were being used as guinea pigs for ‘Western medicine if they are given the medicine, but might feel resentful f only health workers are treated, + Informed consent is an issue as it depends on a level of| ‘education to understand the drug and how it works and. also clarity of thought. People who are dying may grasp at straws bul their relatives may then blame the treatment for an inevitable death. «+ Issues of trust between individuals or communities and health workers especialy if supplies of a new drug are limited. Did youknow? No epidemic but mare ethical decisions Fungal infections can kill people if their immune system is not ‘working well for example, in people suffering fram diseases such as leukaemia or HIV/AIDS, or those taking immunosuppressant drugs Inthe late 1980s the search was on for a new antifungal medicine Chris Hiteheack and his team atthe pharmaceutical company Pfizer set out to design a new molecule that would be more powerful than the existing fungicides and would also kill fungal pathogens resistant tothe antifungal drugs avaiable atthe time. A molecule known as Voriconazole was discovered in 1990 and the long process of development and trialling began. In 1997 there was a tragedy atthe Maccabiah Games, held every four years in Israel As the Australian team entered the arena over afoot bridge across the very polluted Varkon River, it collapsed. Over 100 athletes were injured and four died. Three of these deaths were due toa deadly fungal infection picked up from the river. Sasha Elterman, a talented 15-year-old tennis player, was infected withthe fungus that day. Itattacked her brain and spine and she was given only a 3% chance of surviving. After several months of treatment with every available antifungal medicine, Sasha was sil alive - but ony just ‘Then het medical team read about voriconazole, but i had only just started clinieal tals so was a long way from getting licence. Sasha's doctors got permission to ty it as at this stage she had nothing to lose. Without a different treatment she was going to die. The improvementn Sasha's condition was almost immediate and after 451 days of treatment with the new anti-fungal drug she was fully recovered, [At the opening ceremony of the 2000 Sydney Olympics, Saha Carried the torch into the arena atthe head of the Australian (Olympic team, She was alive as a result ofthe use of anew and incompletely traled medicine In 2002 voriconazole finaly passed allt clinical trials successfully and was licensed. Its stil used cffecively to treat life-threatening fungal infections today. er In any epidemic situation, the ethical implications of using @ fast-tracked and relatively untested drug have to be evaluated at national and international levels, [n the US, the Federal Drug ‘Agency decided that an antiviral called peramivir that had not ‘completed testing could be used intravenously in seriously ill patients in the 2009 HIN3 flu epidemic. The WHO recently decided that ZMapp", which had had no human trials, could be ‘sed in the Ebola epidemic in Western Africa and thar atleast two vaccines could also be fast-tracked through the process for use. ‘The effectiveness of these interventions is yet to be seen, and only then can a ful evaluation be made. 1 "Why the control fhe pea of disease parclary mportntin val diese? 2 What migh be a dsadvartagectgving people a medicine tt reduce the symptoms ofl hea och es Na 3 (a) summarce the main ways in which he spread ofan infectious Soca can be conte 0) Explain why tas pariciry det to conan he spread of the Eolas n Wet cnn 2014 4 (a) ake Row cart show the man stages inthe normal dr development proces, (b) Which stags are mest aly tobe bypassed a drug fst aded foruseih an epidemic? 'S Sugeest why the severity of the disease, the availabilty of other treatments, and the effectiveness of normal disease control ‘measures are such important factors when evaluating whether a new drug should be tried, 6 te a pargpaph soppestng the use ofa new drug that hasnt undergone human tls inthe 2074 Ebola outbreak, and a sir paragraph against each case evaluate the evidence and put forward sienofcaly sound opinors. 7 Anethe ethical considerations for using an uncented trestment the mec diferent when considering the treatment ofa single india! ie Sasha tera ora community suchas thosein Siera Leone Guringan epidemic? Discuss “sy Ebola isa highly infectious viral disease that causes fever and internal bleeding and death in about 50% of cases. The mortality rate isa measurement of the number of deaths in a _iven population ar cue to a specific cause. A pandemics an epidemic that takes place in several counties at 105In 1976 a new and deadly disease appeared in Affica. Ebola virus causes Ebola, a disease that is so damaging to the body tissues that it has a 25-90% death rate. It is both contagious (spread by ‘contact) and infectious (spread by droplets in the ait) and symptoms can appear from 2 t0 21 days. after the initial infection, Reporting on this vial disease varies greatly. fig The deasly From the website of the World Health Organization: Epidemiology and surveillance \W0 continues to mentor the evolution ofthe Ebola ius esoase (EVO) outbreak in Sierra Leone, Liberia and Guinea. Tne Ebola epee tuend remains precarious. Between 21 and 25 July 2014, 96 rew cases ‘and 7 deaths wore reported trom Liberia and Sirra Leona n Guin, {2 new cases and 6 deaths were reported during the same period. ‘These include suspect, probable ana laboretorycomed cases ‘The suoe in the number of now EVD cases n Guinea ater weeks of Jou wralactvty demonstrates thet undetectes chains of transmission ‘existed in the community. This phenomenon... calls for ste0ping UP outbreak containment measures, especially etfectve contact tracing From the Daily Mail: Deadly Fhola virus ‘could spread globally’ after plane brings it to Nigeria ‘Health experts fear other passengers could now he camying the virus ‘+ Telays dormant in victims for upto three weeks ~ and 90 percent die orit By NICK FAG “The news came as it emerged that an American doctor Working for a charity in Liberia had become infected. Dr Kent Brantly, 33, from Texas, had moved to the country for the Samaritan’s Purse organisation with his children and wife, Amber, to help contain the disease More than 1,000 others have been infected by the virus, whi ‘can go unnoticed for thiee weeks and kills 90 per cent of vietins. Follow us: @MailOnline on Twitter From the website of Public Health Wales. Ebola virus disease: an overview [Ebola virus disease isa serious, usually fatal, clsease for which there are no licensed treatments or vaccines. But for people living in ‘counttos outside Aca, it continucs to bea vory low threat. ‘The curentotttveak ofthe Choa veus mainly affects three countries In West Atrica: Guinea, Libera and Sioa Leo. ..This is te largost known outbreak of Ebola, ‘So fa, there has been just one imported caso of Ebola in the UK Exper studying tho virus balove it is highly unikaly the disease wil spree witin the UK, What are the symptoms, and what should | do if think Im infected? ‘person infected with Ebola virus wil typical develop a fever, headache, joint and muscle pain, a sore toa, and intense muscle \weakress. ‘Those symptoms start suddenly, between two and 21 days after ‘bocoming ifactod, but usualy aftr five to sven days. if you foe unwal with the above symptors within 21 days of coming ‘back fom Guinea, Libaria or Sica Leon, you should stay at home anc Immediately telephone 111 er 999 and expan that yournave rst tes West Area ‘Those services wil provide advice and arrange for you tobe seen ina hospital i necessary 20 the cause of your ness can be determined, It telly important that medical srvioes are expocting your arial and cling 111 oF 988 wilensure this happens SON I TEE LE \Where else will | encounter these themes? 106ee Let us look at the different levels of information given in these pieces of writing, and consider who they are aimed at er that a newspape> 3 newspaper 1. The extracts here come from a popular newspaper, the World Health Organization tas tops website and the Public Health Wales website. | ey coecrmisde People to | Pubic Health Wales know ‘| answer. bb, Discuss the different purposes of the three pieces of writing and consider whether | that anyone visiting thei you think they are each fit for their purpose. fies has 2 gemine interest | | in Fincing cut detailed facts || Each of these extracts shows a bias - they are trying to communicate different things. Comment on what each of the pieces is trying to do in terms of informing the readers, | about the topic they are researching! Now let us examine the biology given in each piece of writing. You already know about viruses and bacteria, so you can answer these questions now. If you are going to continue your biology studies 10 A level, you may lke to revisit these pages after you have learned more about communicable diseases in Book 2 Topic 6. 2. Look at the newspaper article and summarise the knowledge about Ebola that you have at the end, How accurate is that information biologically? 3. Summarise what the extract from the Public Health Wales website tells you about Ebola and how you think the virus causes the symptoms of the disease. 4. If you become ill after visting certain African countries, the Public Health Wales website ‘emphasises the need to inform a doctor or any hospital you attend. Why is this so important? 5. The WHO extract gives little or no information about the Ebola virus itself. What is the focus ofthis article? Why is this information also important biologically? Research is key in preventing the spread of viruses like Ebola rent types of vinise Find out as much as you can about the Ebola virus, focusing on how its spread and the way it infects | | ae ways they and takes over the cel of he body Tink careful about which stage ofthe vial ife cycle you woul target to try and prevent the spread Refer to the infomation the disease. | in the Public Health Wales extract and visie the original website as Wel 39 others ard tac | the intormation in youn testo0ok Thi very eateluly about where ana | when a views might be | Winerabe to attack ering Imagine you have to bid for funding to carry out your research, Put together a poster presentation summarising the problem you have identified with Ebola, explaining what you want to research and why: you shoul receive the funding its reproductive2.2 1 The table below refers to some features of prokaryotic and eukaryotic cells Ifthe feature is present, place atiek (7) in the appropriate bex and if the feature is absent, place a cvoss (x) in the appropriate box. Exam-style questions 3 The table below refers to some of the stages involved in Gram staining and the appearance of Gram-negative and Gram- positive bacteria after each stage. Complete the table by writing the most appropriate word or words in the empty bexes, Feature ‘Nuclear envelope Prokaryotic cell | Eukaryotic cell Call surface (plasma) membrane Mitochondria Golgi apparatus [Total: 4] 2 An analysis of the lange organic molecules found in & prokaryotic cell was made. The dry mass of the cell isthe mass of the cell not including water The results of the analysis are shown inthe table below ‘Molecule | Percentage of | Number of | | Number of total dry mass | molecules | different types of the cell/% | percell_| of molecule Protein 550 2.360000 1050 Lipid aL 22000000 4 Glycogen 25 4360 L DNA. aL 2 1 RNA 205 7262480 83 (@) The molecular mass of a substance is the mass of one ‘molecule of that substance. Using information in the table, state which of the molecules has the largest molecular Give an explanation for your answer a (b) Glycogen and protein molecules are both polymers. Explain ‘why there is only one type of glycogen molecule bur there are many types of protein molecule. py (c) Explain why many different RNA molecules are found in a cell (2) [Total: 6] ‘Stage of Gram ‘Appearance of staining Gram-positive bacteria Colourless ‘Appearance of Gram-negative bacteria Colouriess Calls heat fixed onto slide ‘Side flooded with crystal violet ‘Slide flooded with Gram’s iodine ‘Slide sinsed with aleohol or acetone ‘Side counterstained ‘with safranin carbol fuchsin [Total: 4] 4 The table below refers to features of (lambda) phage, tobacco mosaic virus (TMV) and human immunedeficiency virus (HIV). Complete the table by wing the most appropriate ‘wort or words in the boxes. Feature dephage [TMV HIV ‘Type of nucleic acid ‘Shape of protein coat [Total: 6} 5. The table below refers to some structures of microorganisms, Complete the table by writing the name of the type of microorganism possessing each structure in the empty boxes. Structure Nucleus Capsid Flagellum |Peptidosean [ t—i( | pnaeeee Peable to | | spread of Oxford ragwort understencies Ee: | | | spread of Oxtong Wat ht te bio is marin ape? Youre eng armatonwanoverteae | | BME | | questions now, but if you are studying A level Biology you might lke to look back at this when you i Jearn about the way ecosystems develop aver time, and human effects on ecosystems. | University of Onto \ Botan Goris 4. If you investigate the story of Oxford ragwort online, you will find a wide variety of articles including one from Bristol University School of Biological Sciences, Read at least ‘wo articles on this story. How many of the facts had you worked out based on the poem by George Short? 5. What are the elements of human involvement in the story of the spread of Oxford ragwort? 6. What are the adaptations of Oxford ragwort that enabled it to make such a successful ‘escape from the University of Oxford Botanic Garden? Didyou know? ___ Activity Oxford ragwortisso called because itis said to have Asalty survivor escaped from the University of Osfordragwort isnot the only plant wth adaptations that allow it to take advantage of human influences Oxford Botanic Gardena te spread and increase ls range, Danish scury grass ia plan that theives in salty, gritty coastal Portal cetera environments and cif edges Inrecent years thas spree across much ofthe UK - manly along the reer ea tat motorways where it thrives in th salty environment provided by the salting and gritting machines that itundenent a population work throughout winter to keep the roads free from ice, ‘explosion which took it to Investigate the on-going story of the spread of Danish scurvy grass and tel the stony elther as many other places. tis really 2 ee Southem European species, ri land neat relative of the + a newspaper article fr the widest possible audience palin (© From an unpublished colcton of pooms by Goorg Short (publication interrupted by the dat of the author). 16931 1 The five-kingdom classification system is one of the systems, used for classifying ving organisms. (e) Name the kingtiom to which bacteria belong oy (b) Give two structural features found in a bacterium but not found ina virus a (c) Some classification systems consider viruses to be ving orgenisms Give two features of a virus that it shares with living organisms py (q) There are alternatives to the five kingdom classification system, Siggeat wy there's disagreement about ow Iving organisms should be classified py (Total: 7] 2 Classification of organisms is important when trying to assess biodiversity, {@) All organisms can be classified into one of three domains [Name the three domains of organisms. i (b) () Explain what is meant by 2 species a} (i) Explain the meaning of the term genetic diversity within a species. (2 (ii) Describe how zoos maintain the genetic diversity of endangered species. (4) (Total: 11] 3. In the 1990s, a scientist called Woese suggested a new way of ‘grouping organisms into domains. (2) The table below shows Woese's three domains and gives some of the characteristics of each domain Domain | Some characteristics of each domain P “True nucleus absent ‘Small (708) ribosomes present ‘Smooth endoplasmic reticulum absent RNA polymerase made up of 14 subunits Q “True nucleus present Large (80S) ribosomes present ‘Smooth endoplasmic reticulum present RNA polymerase made up of 14 subunits R “True nucleus absent ‘Small (708) ribosomes present ‘Smooth endoplasmic reticulum absent RNA polymerase made up of 4 subunits Exam-style questions () Which of the two domains are most distantly related. A PandQ B PandR © OandR uo) (i) Which domain represents eukaryotic organisms AP BO cR u) (ii) ‘The diagram below represents the phylogenetic tree for the three domains, Place a cross (§X) in the box on the diagram thet correct identifies the eukaryotic domain. fo Time Ancestral forms (iv) Give the name of one of the other two domains. 1] (>) One domain includes the plants and these have cells with a cel wall (i) Describe the structure of a plant cell wall “) {i) A student studied the cell wall arrangement between to adjacent plant cells. He noticed several features ‘which he could not name, Two of these are described inthe table below. Complete the table by writing in the name of each feature described Feature described Site where there was no cell wall and the cytoplasm linked the two adjacent cells Dark line that is the [boundary between one cell and the next cell Name of feature [2] (Total: 10}4. Woese proposed a classification of organisms into three domains called the Archaea, Bacteria and Eukaryota (Eukarya), {a) The table below shows some of the characteristics of the three domains Characteristic Domain ] A B c_| Mitochondiia ‘Absent | Absent | Absent | Cell wall containing | Yes No No | peptidogiyean ‘nino acié carted | Formyk | Metionine | Methionine on RNA that tars | methionine proeinsythesis Sensitive t anibiotes [Yes No No | May contain ves No Yes chorophy () Using the information in the table, suggest which of A,B and C represents the Eukaryota domain. Give a reason for your answer @ (ii) Many scientists believe that the Eukaryota domain is ‘mote closely related to the Archaea domain than to the Bacteria domain Using the information inthe table, suggest which of A, B and C represents the Archaea domain. Give a reason for your answer 2) {) Cells of the Eukaryota domain contain rough endoplasmic reticulum and Golgi apparatus. Both the rough endoplasmic reticulum and the Golgi apparatus are made up of membrane-bound sacs. () Describe how you would recognise the Golg apparatus as seen using an electron microscope. (3) (i) Explain the roles of rough endoplasmic reticulum and the Golgi apparatus in a cel (6) (Total: 13] 5 ‘There are specific differences between the organisms in the three domains suggested by Woese. (a) Identify the names of the three domains suggested by ‘Woese. a) ‘A. Animalia, Archaea and Eukarya B Animalia, Bacteria and Prokaryotae © Archaea, Bacteria and Eukarya D Archaea, Eukarya and Prokaryocae (0) Woese's ideas were not accepted when he fist suggested that every organism could be classified into one of three domains (i) Give two ways in which Woese communicated his findings to the scientific community. a (i) Describe how the scientific community would have evaluated Woese’s theory ia} (ii) Woese suggested that organisms could be placed in taxonomic groups based on molecular phylogeny. Explain wat is meant by this statement (4)Natural selection “The sil bogs is damp and acid with few nutrients, butin North America pitcher plants successfully colonise them - because they are carnivores. Pitcher plants are adapted as pital traps for insects that visit the pitcher as fitwas a flower But the pitcher contains a deadly liquid. Ite dilute acid, because ants attracted by nectar fallinto the pitcher, releasing the formic acid in their body as they decay. The liquid also Contains enzymes made by the plant, bacteria acting as decomposers and a chemical that causes ‘waterlogging of insect wings. Inside the pitcher. downwards facing hairs atthe top followed by smooth ‘waxy surfaces make it almost impossible for insects to escape once they fall into the liquid, where the acid enzymes and bacteria digest them. Some ofthe minerals released are then absorbed into the body ofthe plant. Amazingly, the larva of a species of blowfly actually develops in the pitcher fluid, escaping to pupate but returning tothe flowers for nectar as an adult, so polinating them. The strange flowers ace self sterile, inspite of dropping pollen and nectar onto their ovm stigma. The pitcher plantisa prime example of natural selection, with a mass of adaptations for a bizarre but successful way of life. In this chapter you will consider the theory ef evolution by natural selection and how Danwin's ideas have been modified inthe ligt of our current knowledge of genetics. Through a range of examples, you wil look at the importance of physiological anatomical and behavioural adaptations in diferent organisms, which tenable them to survive and reproduce successfully ina wide range of habitats, If the environment changes. or an individual moves to different habitat, the adaptations that have been successful may no longer work so well. Some individuals ull have extra adaptations that make them better adapted to the new conditions. They are the individuals that are most likely to survive and reproduce successfully, passing on thealleles forthe new adaptation This is natural seletion in action and you will be considering a number of examples. Finally you will be looking at how organisms diverge when they are reproductively separated. As they adapt 10 slightly different conditions in slightly different ways, new species may eventually emerge. You will be Jookingat both allopatric and sympatric speciation, considering examples of bth, Interpret data froma variety of tables and graphs e.g. graph to show effect of adaptations on reproductive succes)gd That there is usually extensive genetic variation in Breer See ees ed Seen eee cee renege are at nat result in the formation of new species eer ner ny eee reer oat ote x eee eee erg Why biodiversity is important and how it can be < ~ peti i peer er eee eC 4 ‘Adaptations in plans and animals for the mass erent Ty i eee eee ad er oe eee aed pressures ee eee Te biodiversity, extinction and speciation (A level) N Sere Tree eet ato) eet eT The way evolution comes about through natural selection acting on variation bringing about Braet Se ete etary niche asa result of physiological adaptations that ere errr et ees Ce eee eee! PeeTTLy Examples ofthe way organisms may occupy a eee eee aed involve their form and structure, making them better adapted for survival and reproduction ere cary Peer eee ae eee ara Ce ee survival and reproduction The ways in which reproductive isolation can lead to allopatric and sympatric speciation aA) '¥ G Se ee ceBy the end of this section, you should be able to.. @ explain how evolution can come about through natural selection acting on variation, bringing about adaptations @ explain how organisms occupy niches according to physiological, behavioural and anatomical adaptations ‘The idea of evolution by natural selection isa ke biology It gives a scientific explanation for the great diversity of life on Earth and for all of the organisms that have existed and ‘become extinct. The idea was put forward by Charles Darwin (1809-82) in his book On she Origin of Species by Means of Natura Selection, and a version of his theory still underpins our understanding of biology today ol ving evolution Darwin spent five years travelling the world on HIMS Beagle, observing the natural history of all the countries where they landed. He began to realise that wherever he went, the organisms he saw were adapted to their particular environment. However, he did get some help from people along the way. For example, ‘on the Galapagos Islands where Darwin made some of his most important observations, the giant land tortoises vary from one island to the next. Each island has a different sub-species and. they have distinctive shell shapes. which are adapted to the and the way the animals feed. The vice-governor of the islands pointed this out, but initially Darwin ignored it. As he noted in his journal, by the time Darwin realised just how varied the organisms ‘on the different islands were, he had already mixed up the collections from the first two islands! On his return to England, Darwin spent the next 20 years or so reading, thinking and honing the ideas his observations had triggered. He carried out experiments on organisms including Pigeons and plants to support his ideas. Final in 1859, he vent public with his theory revatec by ras of the te absorb heat which alone: thm to sui seaweed ancl algae thats abundart on the m4 ies because they are adage x cons of the sands The theory of e lution The main idea of life include: put forward by Darwin to explain the great v + Living organisms that reproduce sexually show great variety in their appearance. + Organisms produce an excess of offspring ~ in other words, ‘many of the offspring an organism produces do not survive to reproduce themselves. AS a result there is always a struggle {or survival, a competition between members of the same species. + Organisms chat inherit characteristics that give chem an ‘advantage in this struggle are most likely to survive and pass on the desired feature to their offspring + Orgenismes chat inherit characteristies that put them at a disadvantage will be more likely a die out before they can reproduc Tis process is known as the survival of the fitest, where mess fs the ability of an organism to survive and reproduce in the environment in which its living. Darwin called this process natural selection. \When the long-term changes in organisms that occur as @ result of natural selection produce a new species, this is evolution. Evolution is a change in the genetic composition of a population of organisms over several generations. as a result of natural selection acting upon variation, bringing about adaptations and in some cases leading to the development of new species. The variation may be the result of sexual reproduction, random ‘mutation, inbreeding or hybridisation. Did youknow? Friendly competitors ‘Alfred Wallace (1823-1913), another British naturals, proposed a similar theory to Darwin - in fac they each published an iia paper atthe Linnaean Society atthe same time. However, Darwin's ideas ‘were backed up by a much greater bank of research and observations, and he published his book on the subject first ~ and so itis Darwin ‘who is mainly associated with the theory of evolution. However, Darwin and Wallace always remained in contact and Darwin helped ‘organise a pension for Wallace when he fell on hard times. rwinism - evolut first century ion in the ‘When Charles Darwin developed his theory of evolution by ral se DNA, genes and the genetic basis of the variation in living ‘organisms. As our knowledge of genetics, genomics, molecular biology, ecology and palacontology has grown, our model of evolution has itself evolved. ion, no-one had seen chromesomes or knew about‘A modern statement of the theory of evolution might be: The evolution of organisms occurs as-a result of the aifforeral ferity and survival of organises with differen genotypes (genetic variation) leading to diffrent phenotypes within a specific environment. Those alleles that deliver the adaptations best sulted 10 the environment are ‘most likely to be passed on tothe next generation. ‘This more madem definition suggests that a disadvantageous trait does not necessarily mean those indwiduals are wiped out. They ‘may simply be less successful at reproducing. It also recognises that the advantages or disadvantages of a particular trait will «iffer with the environment. The changes in the frequency of a particular allele in a population of organisms, which may or may not lead to speciation, are almost always driven by a change in the ‘environment or by the organism moving into a slightly different ‘environment. Learningtip Make sure you are very clear about the difference between natural selection and evolution. Natural selection isthe process by which evolution occurs, but ‘natural selection does not necessavily lead to the evolution of anew species. Adaptation to a niche (Organisms do not exist in a vacuum. The various species ar all patt of a complex system of interactions between te physical ‘work and other living organisms that we call ecology. Each spetis exit ina particular niche ‘The niche occupied by an organism is an important concept that is dificult to define. Ic describes the role of the organism in the ‘community ~ rather like a job description or a way of life. You can ‘consider different aspects of a niche, such as the food niche or the habitat niche. Some niches are very large and general, for example ‘organisms that eat grass; some are very smell and specific, for ‘example organisms that feed by cleaning the teeth of other. larger organisms, Successful adaptation ‘A successful species is well adapted to its niche, meaning that individuals in that species have characteristics that increase their chances of survival and reproduction, and therefore of passing those characteristics on tothe next generation, Adaptations may be of many different kinds including anatomical, physiological and bebaviowal + Anatomical adaptations involve the form and structure of an ‘organism, for example the thick layer of blubber in seals and ‘whales, and the sticky hairs on the sundew plant which enable it to capture insects ready to digest. fig The sow 0 EE fig B Tho sicky hale ofa sundew are anatomical adapiavons thas erable the pnt to eapn ieee and ute ther bodies 0 spplement the afents inwhen t gros. + Physiological adaptations involve the way the body of the organism works and inelude differences in biochemical pathways or enzymes, For example, diving mammals can stay ‘under water for far longer than non-diving mammals without drowning. Once they are under water their heart rate drops dramatically so that the blood is pumped around their body less often and the axygen in their blood is not used as rapidly (Gee fig C). The main body muscles ean work more effectively using anaerobic respiration than those of landb-iving mammal, so the oxrygen-carrying blood is directed to the brain and the heart where itis still needed. This is known as the mammalian diving response. 120 160 140 120 100 80 60 40 20 o. 0903 03 OF 15 21 27 33°39 45 51 ‘Time/min te/beats perminute Hear + Behavioural adaptations involve changes to programmed or instinctive behaviour making organisms better adapted {or survival, For example, many insects and reptiles orientate ‘themselves to get the maximum sunlight on their bodies when the air temperature is relatively low. This allows them to warm up and move fast enough to feed and to escape predators. When they get hor, they change their orientation to minimise their exposure to the sun, or shelter from it, Social behaviour such as hunting as a team or huddling together for warmth can improve the survival chances of both individuals and a group of organisms. Migrating to avoid harsh conditions, courtship rituals and using tools are other examples of behavioural adaptations, WsSuccessful adaptations enable species to exploit every p habitat and the different niches within each organisms have a mixture of different types of ac that enable them to survive and succeed in their particular Fungi are often thought of as saproohytes, breaking down dead fever, sore fung. r active carnivores sin the soil. Some found in huge nun environment. Here are just a few examples: ‘groups of fungi have developed adeptations that enable them tc Capture and feed on these nematodes. Some produce sticky ne C i ! adhesive pads to rap the worms, some live inside the living 3s, but Arthroboirys anchoniais a fungus that actively lassoes : remato called constriction When grayling butterflies ly, we can see their beautiful wing: rings as they pass. involving both structural and physiological Yowever, the und the wings i a dull, broken patter adaptations (see fig B) Three fungal cels form a ring and when of greys and browns This anatomical adaptation gives them 4 nematode moves into it, a combination of wall changes and the smouflage against the coastal heathlands where ‘osmotic potential of the cells result in water mewing in fast. Withi come almost invisible when they land, 0,1 seconds the ring infiates and holds the nematode in its grip. on sunny days, their shadows could make them visible Often the nematode puts it til through another loop as it moves ators. They have a behavioural adaptation that allows them to try and escape. Within hours the fungus nore hyphae to overcome this they follow the sun, changing their orientation hat penetrate the body of the nematode and absorbing through the day so their shadow is always as small as pos the nutrients and transporting them within the fungus. [is thought This also helps to contrel their body temperature, preventing that these predatory fungi evolved f ytic Fung! in a high from ovetheating as they absorb es litle heat as possible. A carbon, low nitrogen environment. ‘The nematodes provide the variation of the same ad hat if they need to warm — missing ni up to fy. they will risk bei and angle their wings to absorb — more of the heat from the sur ey tation meat fg Some carnivereus fung have adapsaions hat enable ther to lass0 the! e t nt, d eam looked at the relative importance of physiological and behavioural adjustments in the great cormorant (Phalacroco ) in bo contrasting, environments ~ Normandy, where the water temperature 12°C, and Greenland, wihere itis 5°C. Cormorants are not wel insulated by fat and have poorly waterproofed feathers so they are easily affected by cold. The team found big differences in the feeding behaviour of birds breeding in the two regions. The birds living in Greenland spent 70% less time in the water than those in Normandy. They spent far less time swimming on the surface Cf the water between dives, and also returned ta the land more en. The total & both areas, b ly energy intake of cormorants was similar in ure rates in Greenland were 150% higher ey‘than those in Normandy because the changes in their behaviour resulted in far greater efficiency at finding food, Behavioural adaptations were more important than physiological ones to their survival in the colder niche. fig Handing cormorants needs care ad sil but the wor of and his eamhas gen usa beter understanding ofthe be ‘advrations tha crabie these and brad Natural selection leads to adaptations that give individuals an advantage in a particular niche. If conditions change, those adaptations may nos be as successful, and the selection pressure ‘wil change. This may lead to changes in the species, and ultimately tothe formation of new speci Compare Darwin’ original theory of evolution with the more ‘modern version ofthe theory and explain the differences 2. Evolution is based in parton adaptation. Discuss what is meant by adaptation and whether the different types of adaptation can really be looked at in isolation, 3 Explain the importance ofthe niche concept in understanding the adaptations of organisms. Looking atthe data from fig C, answer the following questions: (a) Whatdo the negative numbers on the x-axis represent? () How long did the recorded dive last? (@) What was the percentage depression of the heart rate? Based on this how long would you predict that the dive might have. lasted without the bradycardia? (¢) Describe the type of adaptation involved in this response and explain why itis so important to the survival ofthe seal in its ecological riche How do the behavioural adaptations of cormorants in Greenland help them to survive in thei cold-water fsh-eating niche? Natural selection is the process by which the organisms that are best adapted in a particular environment are most likely to survive and reproduce, passing on their advantageous alleles o their offspring The genotype isthe genetic make-up of an organism with respect to «a particular feature Phenotypes are the physical traits (including biocherical characteristics) expressed asa result ofthe interactions ofthe _Renotype with the environment Aaallele is version ofa gene, avariant Ecology is the study ofthe interactions of organisms with each other ‘and with the environment in which they live, ‘Aniche isthe role ofan organism within the habitat in which ilives An anatomical adaptat structure of an organism. A physiological adaptation is an adaptation involving the way the body of the organism works, including differences in biochemical pathways or enzymes. 3 isan adaptation involving the form and) ‘A behavioural adaptation is an adaptation involving programmed or instinctive behaviour making organisms better adapted for survival WwNatural selection in action By the end of this section, you should be able to.. @ explain with examples how evolution can come about through natural selection acting on variation bringing about adaptations Individuals tha are nor well adapted to their environment may not survive to reproduce or may produce fewer offspring than those that are better adapted, so their characteristics will Become less common, inthe population. This is what is meant by the term ‘survival of the fittest” and is what Charles Darwin called natural selection. I the niche occupied by an organism changes due to changes in the environmen, different charaeteristios may make an individual more successfil, Natural selection wil favour the survival of individuals ‘with those diferent characteristics, and we say the selection pressure has changed, Changes in selection pressure result in changes (evolution) within the species. Depending on how diferent the individuals are, they may even be considered a new species. Oysters adapting to change Malpeque Bay on Prince Edward Island in Canada is home to ‘massive oyster populations (Crassostrea virginica) In 1915 the oyster fisherrnen of Malpecue Bay began to notice that amongst their usually healthy catches there were a few diseased oysters that were small and flabby with pus-filled blisters. Before long the oyster beds had been all but wiped out by this new Malpeque disease, However, a small number of the millions of oflspring produced by each oyster {in a year carried an allele giving them resistance to tae disease, ‘Because only indivicuals that had this allele were able to survive and reproduce, the frequency of this gene in the population increased rapidly: By 1935 a small oyster harvest was again possible and by 1940 the beds were as proiic as ever, but with a rather differed gene pool — now containing a high frequency of disease-resistance alleles (see fig A). These oysters were nota different species ~ they ‘were stil C. virginica ~ but they had adapted by natural selection to a changed environment. 7000 000. 5000 4000 3000. 2000 1000. Oyster harvest barre! 0. 1915 1920 1925 1930 1935 1940 1945 Year fig A Opteryelts fom Malpeg populations, But asa esl ofthe increase resstance alslewithin Disease devastated the jection ofthe disoxe 178 Natural selection in moths Bernard Kettlewell (1907~79) at Oxford University in the 1950s studied the peppered moth Bision betularta and proposed that the moth had undergone natural selection in response to environmental changes, The normal, or ypical, form of B, bewlaria isa creamy speckled moth found in British woodlands. In the eighteenth century, black specimens or melanies resulting from a random dominant mutation were captured occasionally. They ‘were easily visible against the pale bark of the trees, bath for Juman collectors and for birds looking for a meal. This selection [pressure meant that the frequency of the dark allele in the population remained low. ‘Then in the mid-nineteenth century soot and smoke ftom the factory chimneys of the Industrial Revolution darkened the bark of the trees and the surfaces of buildings. As a result the melanic form of beiwlaria was at a selective advantage and the frequency Cf the allele within the population began to increase as more and more of the light-coloured moths fll prey to predators. This process became known as industrial melanism. Kottlenell set up several experiments to examine the selection of the two forms. In an unpolluted area with clean trees in Dorset he released equal numbers of light and dark moths; 12.5% of the light moths were subsequently recaptured, but only 6% of the dark ones. In other observations birds were seen to eat 26 light moths and 164 dark ones as they rested on a ight tree trunic In Birmingham, atthe time a highly polluted industrial area, 40% of the dark moths were recaptured, but only 19% of the light ones. Of the moths picked off the blackened trees from equal releases, 43 were light and L5 were dark. Kettlewell concluded that the ‘change in frequency of melanic moths was due to the selection: melanie moths had become the dominant form,Reversing the trend Anti-polution legislation that was passed in the 1960s resuted in cleaner, pler buildings and trees again, so the selection pressure has moved back in favour of the paler moth (see fig C). The fiequency of the ypical or pale alee in the population has increased again ‘There is evidence for similar industrial melanism in over 70 different species of British moths. For ‘example, the melanic form of the marbled beauty math Cryphia domestica was dorninant in London in the 1970s and 1980s but, since the 1990s, the pale form has reappeared in strength 200 km & & fig The map on the eft shows the proportions ofthe melanc maths inthe population from Ketlewalls 1956 data The mapon the right shons data on mots colcted in siniar areas by Bruce Grant and Wscoleagues in 1956. Selecting for reproductive success Sometimes natural selection operates on adaptation hat are less do with survival ina particular habitat than vit atrocing a mate. For example, male Aficanlongetiled widow birds have very ong tals that appear to have very ile use except inthe mating season to atract mates. To investigate this mae bids were captured and tei tas artifical Iengihened (by ging extra eaters on) or shortened (by cutling them). Once released, their reproductive success was measured by the number Of nest with eggs and/or young inthe terioy ofeach male. The birds wit artifical lengthened tly were cary the most sucess (se iB) Males whose tails were artifically lengthened attracted more females, ‘and had greater reproductive suc than males with normal or shortened tails, or the control group Average number of nests per male ©" Imilicially Normal Control Arifcially lengthened shortened fig D The clection of an anatomical adapta long-talet wdow bids The conta go age in grtnga mate canbe sean in ican fc ther tall cut and repsied wth gue Many animals show similar selection for features that give no advantage within their niche, but are linked to reproductive success, for example the thick skulls and enormous horns of some antelopes, fig The amazing tern and and the spectacular tal of the peacock. Plants also show some amazing adaptations. All insect- sructies ofthe bee orci pollinated flowers have adaptations to bring pollinators to the plant, but they have not al evolved to have no benefit the pane the level of the bee orchid, which is adapted to look lke a bee, excepéto ata bees to polinate the flower and so ‘ensue reproductive succes, 179180 Directional selection The oysters of Malpeque Bay and the moths of the British woodlands are good examples of directional selection, ‘classic’ natural selection showing a change from one phenotypic property to anew one more advantageous in the circumstances, Directional selection occurs anywhere that ‘environmental pressure is applied to a population, The introduction of the rabbit disease myxomatosis into Britain in 1953 is another example. It almost ‘wiped out the rabbit population over the following ten years, but rabbits are now common once: ‘more, Many of them carry an allele that renders them immune to myxomatosis ~ the frequency of, that allele in the rabbit gene pool has increased enormously. 1 How can changes in a niche or habitat lead to changes in a species? N Using the data from fig A, how long cid it take for Malpeque disease to virally wipe out the oyster ‘population i the bay, and how long ci it take forthe resistance allele to become sufficiently dominant forthe population to recover? Why's this an example ofthe adaptation ofan organism to its niche? 3 elavalyrceny, some cess calenged Ktewal slogan ideas aboutindstil mln, Even tore een many move cents havesapprted is wort and the or of beta ogre dane ofthe bes dorumented examples of icustl melanism ing thlsseon the support materi tnd ay other resources you have vestigate the evidence or and apust ins maaan based on i seul Key definitions Selection pressure is the pressure exerted by a changed environment or niche on individuals in a Population, causing changes inthe population asa result of natural selection. Industral melanism isthe evolution of dark-coloured individuals in a habitat that has been made darker by industrial polltion, eg. soot, Directional selection is natural selection showing a change from one dominant phenotype to anather in response toa change inthe environment ~ one phenotype i selected for over al the others. A gene pool sll ofthe alleles of all ofthe genes in a population,The evolutionary race between pathogens and medicines By the end of this section, you should be able to... © Explain the evolutionary race between pathogens and the development of medicines to treat the diseases they cause Maration, adaptation and natural selection are not only seen in eukaryotes such as the cormorants, fungi and moths you have considered in the previous chepter They are also seen in pathogens (disease-causing organisms) such as bacteria and viruses. AS a result the medicines that we develop to destroy pathogens can quickly become ineffective. The pathogens are in {an evolutionary race against us and the medicines we develop to treat the diseases that they cause. Beating bacteria, step 1 Bacteria cause a wide range of disesse. rom throat infections to tuberculosis and septicaemia. We ha no medicines to care bacterial diseases on a large scale until the mid1940. Before then, milion of people died globally every year asa result of bacterial infections. When the werkeof Alexander Fleming, Howard Florey and Ems Chain resulted nthe mass production of penicilin, the effect ofthe drug seemed almost miraculous. People recovered from infections that would have meant certain death and everyone ‘thought har the bale against bacterial disease was won. However the discovery and development of penicillin was the beginning of the antibiotic story. not the end. Penicillin didnot Kill all of the different types of bacteria. As you saw in Section 2.2.1, the peniciln family of antibiotics affect Gram-positive bacteria, ‘with their thick peptidogiyean walls, but do not affect other bacteria. A range of antibiotics were developed that targeted different types of bacteria and fora short time it appeared that bacterial diseases would become almost a thing of the past. Antibiotics were prescribed freely and everyone came to expect, an antibiotic prescription when they went to the doctors with an original population bacteria with resistant includes some ‘mutation more likely mutations to survive infection, It is estimated that, on average, antibiotics add 20 years to each person’ life in countries lke the UK end USA. Bacteria fight back Asign of the problems to come emerged rapidly. Within a year of peniciln fist being used as a medicine there were reports of penicilin resicant Staphylococcus aureus. By the 19605, mary bacteria had become resistant to penicilin, A tiny percentage of the original bacterial populations (estimated at about 1%) must brave carried a random mutation (see Section 1.3.6) giving them resistance to damage by penicilin. In many cases the adaptation, ‘was the presence of an enzyme called peniciinase that splits the pericilin molecule so it no longer works. This adaptation gave the bacteria a great advantage and so, asa result of natural selection, resistance to penicilin became more and more prevalent in ‘bacterial populations. Once again, people became seriously ill and died from bacterial infections that were no longer affected by pericilin Beating bacteria, step 2 ‘As peniciinresiance spread, scientss proiced anew antibiotic called methiclin This pur people ahead again nthe evotutonary Face against pathogenic bacera as common pathogens had fo resistance to mehiiin However tis ddr last ong and relhcilin resistance spread rapidly trough bacterial populations, and now the antibiotic has few uses. Resistant pathogens such as methicinsesistant Staphylococcus ures (MRSA) area sorious problem in hospitals and are homes in many dierent counties {see Book 2, Section 6.1.6), The bacteria were ehead epain Ate moment there ae growing manbers of bacteria that ae resistant to not just one but many antibiotics. These mul-resstant sttoins of bacteria are almost unreaable. Some are even resistant to vancomycin, one ofthe most powerful anthiotcs we hav. ‘which stil cures the majority of setous bacterial infections zew population almost entirely resistant to antibiotic antibiotic taken, apart from new mutants, oe aayee g tafe ae antibiotic taken new population has higher proportion containing the advantageous only bacteria with resistant mutation survive resistant mutation fig A The evolution of anibiouc resistance by natural election, 1811980 1990 Theis in MRSA and vancomycin how Fic bacteria ae geting ahead in redicines we have rae thea 2000 tant enterococeus (VRE) shows we evolutionary face against the senses they cau. penicilin 1347 1942 vancomycin 1356 2002 (partial resi ‘methicilin 1960 1987 linezolid 2000 2001 dapromycin 2003 2005 tigecycline 2005 2012 ‘able A The speed a which bacterial esstance has developed to aa amibiots, What does the future hold? Unless things change, the future could look very bleak ‘There are serious fears that we could return to a time when bacterial diseases are cone of the biggest les inthe UK. Not oniy is antibiotic resistance ‘nereasing, but the number of new antibiccis being developed and ‘brought onto the market has been steadily falling (se fig C) gE» 2 Fess E oe6 ool E oe E i3 = PEEPS S fF SF SS 6 FE KK SS fig The fallin the number fnew antoties approved for use bythe FDA the USA Factors that contribute to the problem include: + Antibiotics are too widely prescribed and used. + Wide-spectrum antibiotics are often used to make sure they have an effect rather than testing to determine if an infection is bacterial and if so which bacteria are involved, + People do not complete courses of antibiotics, which makes it easier for resistance to develop. + In.some countries antibiatis are widely used in the food chain. + Alack of basic hygiene in hospitals and care homes has encouraged the spread of antibiotic resistant organisms such as MRSA. + There is no big financial incentive for pharmaceutical companies to develop new antibiotics as new antibiotics will be used sparingly to prevent the development of resistance. 182 Although bacteria appear to be getting ahead in the evolutionary race, we humans stil have a few tricks up our sleeve. Here are some cf the ways in which we hope to overcome the problems of antibiotic resistance and maintain effective antivacteral therapies for the future: + Reducing the use of antibiotics. + Better education so people understand that they do not alnays need antibioties, + Reducing the use of antibioties in farm animals + ‘The Longitude Prize 2014 sot the challenge to develop a quick test ‘confirming bacterial infections in the docter's surgery, making it ‘easier to prescribe the best antibiotic for maximum effect. + DNA sequencing will help identify bacteria and find new ways of targeting them with antibiotic drugs, and genetic engineering vill enable large amounts of new drugs to be produced. + Development of new antibiotics: Scientists are locking ata wide range of substances that show antimicrobial properties in the natural world and designing new molecules using computer ‘modelling, In recent years scientists have looked at chemicals in places including the blood of crocodiles, honey, sol fish slime and the deep ocean abyss to ty and find novel antbiotcs. ae. figo Trew pred repionyces pacer, colectes In Pace Ocean sediments, ice compounds may ave us a complete naw case ot Anubiovcs- the avadimyecns, Scns nk he new drugs may be (fective against aritaxand possibly MRSA. If you continue to study Biology A level you will learn more about the evolutionary race between pathogens and the development | (of medicines to treat the diseases they cause, including the ‘mechanisens of resistance 1 expan hewarmtaton can re onebactatom an ange evr otha ohesame ype 2. Producea fow dlagam to explain how antboterestance devlopsin«popuaton of cclena 3. Explain how the following lead to the development of antibiotic resistance: {a} overprescribing antibiotics (0) individuals who do not complete their course of antibiotics. 4. someone winsthe Longue Prize. dcsshow this nverton could reduce the development of antbiotc resistance in bacteria fou Aesistant bacterium isnot affected by an antibiotic.Speciation By the end of this section, you should be able to... © explain how reproductive isolation can lead to allopatric and sympatric speciation ‘Changes in populations of organisms are very interesting and they cantell us a great deal about the process of natural selection, But 2 species is usually a much bigger entity than a single population, and often consists of a lage number of populations spread across ‘country or even countries. So how is a new species formed? Isolation and speciation ‘A species is group of organisms sharing a ruber of struct and evolutionary features, which are capable of intebreeting 0 produce fer ofspring Speciation. also Krown as the formation of a new species, happens as a result of the isolation of parts of a population The ky factor in he process srpradutv solton. ‘The rwotoeted populations emperence dierent conditions, and thisin un means tat natal selection acts in diferent rections on the two populations As result, overtime both the genotype and the phenotype of the nolated groups il change. This can continue to the point where, een if emer of the spit population are reunited, they can no longer successfully interbreed. Speciation can also take place as a result of hybridisation and. this is particularly common in plants. Sometimes two closely related species can breed and form fertile hybrids that are successful in their own right and may be better adapted to the niche. In some cases these hybrids do not produce fertile offspring if they are crossed back to their parent plants so @ new species is formed, which may out-compete the parent plants, for example, the hybrid formed between native and Spanish bluebell Isolating mechanisms For diferent species to evolve from an orginal species, erent populations of the species usualy have to become reproductely Solated ffom each oer so that mating and therefore gene flow Between them predicted There ate a numberof way in hich this ay happen + Geographical isolation: apical barter suchas tverora "mountain range separate individuals fom an orginal popalaon. + Beological isolation: two populations inabit the same region, but develop preferences for different parts of the habitat + Seasonal isolation abo known a temporal isolation ihe Fmning of flowering or sexe] epveness in some pais of @ opultin its avay fom the norm forthe group. Ths can ental lead tothe two group eprdocing several months apart + Behavioural isolation: changes occarin the courtship ritual display or mating pattem so that some animals Go not recognise others as being potential mates. This might be due to ‘mutation that changes the colour or pattern of markings. + Mechanical isolation: 2 mutation occurs that changes the ‘genitalia of animals, making it physiclly possible for them to mate ‘successfully with only some members of the group crit changes the relationship between the stigma and stamens in flowers. making pollination between some individuals unsuccessful Reproductive isolation is the key factor in speciation. Allopatric speciation Allopatric speciation takes place when populations are phyrtcally or geographically separated in some way Seintsts Tecognise allopatric speciation as the main evoiionary process. ‘Allopetric speciation is of enormous importance inthe history of evohtion, es great land masses moved and separated. The psical isolation of populations continues to occur asa rest of natural changes, for example as islands form and disappest. as ice floes mel, rivers change course and lakes either dry up or appear ~ and so allopatric speciation continues tobe very important. Some ofthe changes that result In llopatc speciation ae the result of human interventions such as dams, roads and cies. ‘There are many examples of allopatric speciation. Some of the ‘most striking are when organisms become completely isolated — for example when islands are formed, When a species evolves in ‘geographical isolation and is found in only one place itis said to be endemic. Endemic species of Madagascar Madagascar. a large island off the coast of East Africa, prvides good examples of endemism as a result of allopatric speciation, ‘Almost all of the species found there are endemic tothe island. “These range from the amazing giant baobab tres to ringetailed lemurs and from the bizarre elephants foot plant o a small, ppoifcally breeding mammal, the tiless tenrec which can have cover 30 babies ata time, The only species that are not endemic have been taken to the island by people in relatively recent times Imported species ean cause many problems to the endemic species fig A The ring-aled lemursjust ane ofthe unigue species endemic to Mailagascar a a reault of aloparic specaton. 183Desert pupfish Inthe Nevada deser, close to Death Valleys the Ash Meadows National Wildlife Refuge. At one stage this area had many springs. streams and rivers, bu around 50 O00 years ago the climate changed and the area became cry and ari Most of the water cried up, but small individual ponds and springs emained The fish tapped in each area could no longer interbreed and evolved independent Now in this oasis there are four completely separate species of desert pupfish, each with different colouring and different courtship, displays each endemic to one place. They are the Ash Meadows Armagosa pupiish, the tiny Devils Hole pupfish, the Warm Springs pupfish and the Ash Meadows speckled dace. The Devils Hole is pethaps the mast excreme of the tiny ecosystems ~ the fish there Ihave adapted to survive in warm water that rises and fll when ‘there are earthquakes in Mexico figB (a) Devis Hole and (b) Deis Hole pups Adaptive radiation Allopatie speciation is fequenty flowed by adaptive radiation. Adaptive radiation takes place when one species: cles mpidly to form a numberof diferent speces, which all fil diferent ecological niches There area numberof welHimown eamples of adeptve radiation: + Australian marsupials and monotremes: Australi is wel- ‘now forts unusual fauna and flora, Pethaps most unusual are two groups of mammals, the marsupials, which protect their young in pouches, and the evn rare eg laying monotremes. inthe rest ofthe wo, the placental mammals dominate. Until about 55 milion years ago, Ausala was joined to the restof the world when the only mammal were marsupials and monotremes, Aer Australia separated fom the cther Continents, the marsupials evolved tofillan enormous range Of riches, from the aig herbivorous kangaroo with ts wide- ranging niche to the koala with its eucalyptus tree niche, and others with diferent carnivorots riches, for example the qqol and the Tasmanian devil On other continents placental ‘mammals evolved and mostly replaced the marsupials and ‘onotremes but they di not reach Austaia uni humans arrived, eventually binging otter mammals with them, + Darwin's finches: hesebirds provide a dassc example of how the availty of a range of diferent niches produces diferent selection pressures and results in adaptive radiation. The finches were dscovered by the great nineteenth century natualst Chatles Darwin on his woyage on Fas Beagle. On the Galapagos Islands near the equator there ae anamber of feeding riches 184 {fig The unique fauna of Australia sal te rest of alopatrec speciation ard adaptive radiation as a fest ofits geographical soaion {or birds, for example small seeds, lange nuts and insects living inrotten bark. The original inches that arrived on the islands ‘were of a single species. No-one is quite sure how they got there because the islands are 500 miles from land, but a small lock ‘was probably carried there by a storm or a hurricane. Within the birds that arrived atthe islands, there would have been variation in alleles and characteristies, and ferent niches on the islands would have favoured individuals with diferent variations For example, a bird witha slightly smaller, stronger bill would get more food by eating mainly seeds, ‘This would enable it to thrive, reproduce and pass cn its beak characteristics to its offspring, Over generations, natural selection resulted in individuals with small strong beaks ‘ideally adapted to eating seeds Similarly a finch with a longer thinner beak might well be more successful in prebing dead ‘wood for insects and so begin to feed relatively exclusively in that way: By exploiting different niches the finches avoided competing for the same relatively scarce food resources. AS @ result, at least 14 different species of finch have evolved on the Galapagos Islands over several million years trorn one common, ancestral species, Because food was such an important selection pressure, i ‘was important to mate witha finch with a similarly shaped beak to pass on the advantageous characteristic. Mating with 2 finch that had a differently shaped beak would produce a variety of offspring that were less well adapted to feeding, so there was a selective pressure on choosing the right kind of sate, As a result any phenotypic and behavioural changes that ‘made choosing the right mate easier were also selected. so the diferent species look different. Although the finches specialise ‘and feed on particular types of food, and vary considerably in size and appearance, DNA analysis has shown that genetically they are remarkably similarfig Over several millon years at east 14 spies of finches evalved from the orignal anceser species The anatomy of The beaks and adaptations or feeding of 10 ofthese finches shown n ths agian. Sympatric speciation Sympatrie speciation takes place between populations of a species ving inthe same place that become reproductively isolated by mechanical, behavioural or seasonal changes. Gene flow continues to some extent as speciation takes place ~ a very different model to allopatric speciation Sympattic species are closely related and occupy overlapping ranges. Many scientists are reluctant to classify examples of sympatric speciation, suggesting that when speciation occurs there is always an adaptive pressure, including the presence of unrecognised microhabitats, which drives the formation ‘of two species and produces a barrier between the populations. DNA evidence often shows that species originally thought to be the result of sympatric speciation actually show evidence of cross breeding or geographical or niche separation at some point. Sympatric plants ‘There are two species of palm tree endemic to Lord Howe Island in New South Wales, which appear 10 be an example of pure sympatric evolution, although opinions differ between researchers on ths, _Howea forsteriana and Howea belmoreana diverged from each other a very long time after the island ‘was formed 69 million years ago. The island is so tiny that geographical isolation is not possible. The ‘ees are wind pollinated and produce lots of pollen so they could interbreed if they were not separate species. The type of soil they grow on seems to influence the timing of flowering and could be the driver for the speciation. DNA evidence supports the theory of sympatric speciation for these trees Sympatric speciation in progress ‘There appears to be an example of sympattie speciation in progress in the United States. Unt the mid-1800s the tiny fruit fly Rhagolers pomoneta lived only on hawthorn bushes, laying eggs on the fruits The larvae respond to the smell of the havithorns and return as adults to henthorns to reproduce. However, over 150 years ago along the Hudson River Velley many huge apple orchards ‘were planted, Genetically apple trees are quite closely related to hawithorns. Some female pomonella laid their eggs on the apples either by mistake or because they could not find hawthorns The larvae did not do particularly well,but some survived to adulthood. These fies, responded tothe smell of apples, not hawthorns, and a breeding group of apple-dwelling fies evolved. Now there are two breeding groups of pomonella in the Hudson River Valley. One feeds ‘on havithorns, the other on apples, The two populations show increasing reproductive isolation because they mate oniy with fies on the same food source. The apple-cwelling fies have adapted to life on apple trees so they now emerge from their pupae at a different time of the year (see fig E). Apples provide more food and better protection forthe maggots from parasitic wasps. Scientists have analysed the frequency of a number of alleles in the flies and have found they are becoming 185increasingly different. It seems likely that two entirely different species will evolve, which will no longer interbreed as their reproductive cycles will be completely out of synchronisation, apple fruiting apple race hawthorn race i [hawthorn fruiting ‘Total fies emergent UTI SURE % 15.25 5 15.25 5 15 25 8 15.25 5 15.25 5 15 25 June July Aug Sept = Oct. Nov fig The apple ace of fies now emerges enrlrthan the hawthorn ree 50 there wl be less chance a iterbeed ard a greats chance that ts will lead to sympatric speciation (ata from Reng 19 and Fichok 1999 _ Cichlid fish in the African lakes ‘The cichlid fish of the Afican lakes are an example of speciation ona grand scale, illustrating allopatric speciation, adaptive radiation and sympatric speciation. ‘The family Cichlidae contains an enormous variety of fish, including tilapia, an increasingly important source of protein for many people in Africa and around the world. Cichlids show immense variation in shape, size, colour feeding habits, courtship displays and breeding habits. They include a number of species, that are mouth-brooders, which means they carry their eggs in ‘their mouths until they hatch and then allow the tiny fish to retreat ‘back into cheir mouths when danger threatens, ‘ale is a largely enclosed environment, so within a lake there ‘willbe many different habitats and ricrohabitats, but no readily available way of moving on to another lake except under exceptional circumstances such as major flooding. As a result, speciation takes place within each lake independently. Within the individual great lakes of Altica, the cichlid fish have undergone speciation and adaptive radiation to produce an amazing variety of species overtime. Scientists have not yet found and identified al of the species of cichlids that live within these enormous bodies af water There are he divest ofthe species of cichlids in Lake Malaw probably around 1500 species of cichlids within Lakes Victoria, ‘Malawi and Tanganyika alone, and the evidence suggests that in Lake Victoria at least, much of this speciation has taken place cover the last 15 000 years, Cichlid speciation ‘Molecular phylogeny suggests that the great majority of the Cichlid fish evolved much more recently than the lakes were formed, The fish in each lake are more closely related to the other species of fish endemic in their own lake than they are to the fish in the other lakes. This suggests that the fish have diversified in the individual lake systems after they have become separated from each other: + For example, in Lake Malawi, DNA evidence suggests that all of the species have evolved from a common ancestor within the last 5 million years. They have less than 6% difference in their mitochondrial DNA (see Section 2.1.3). The original ancestor is thought to resemble the swamp-cwelling fish Astatoilepia calipiera, which isthe only one of the eichlid species found in Lake Malawi that js also found in other lakes, + This ancestral species fed by sifting algae from the mud sediments at the bottom of a swamp or lake, The cichlids that now fil the lake have evolved to fil almost every available seeding niche in a living example of adaptive radiation on fa grand scale, There is a species that removes and eats the parasites from the skin of catlish, which also lve inthe lake. ‘There are cichlids that eat scales, that bite fins and that eat the eggs and young of other cichlids. Some live at great depths and have very large eyes to see in the dimmest light Others feed on insects that land on the rocks atthe edge of the lake and have eyes and other sense organs that work in the air as well as the ‘water Some species eat crabs, some snails, some rasp algae off socks and some eat plants. ‘The evidence suggests that these different species rarely interbreed in spite of living in the same lake + Lake Victoria is much younger than the other two big lakes, ‘and scientists know it has dried out three times during its 400 000-year history. The last time it refilled was only 15000 years ago. The few cichlid species that survived the dry period, hidden in the mud or in tiny remaining pools of wat have evolved to produce the 500 or more species scientists have so far recorded in the lake today. By identifying micro- environments and looking atthe alleles that have changed, scientists are unravelling the selection pressures that have driven this vast and rapid evolution, They have discevered, {or example, that the cloudiness of the water can drive the evolution of species with very similar feeding habits. The water gets cloudier with depth, and this affects the wavelength of light that penetrates. Research shows that species living in deeper and claudier water have different optical pigments in their eyes than fish with similar feeding habs living in the clearer, shallower water The females are less affected by colour in their choice of mates, and the males tend to have red and yellow display colours ~ wavelengths of light that penetrate the ‘loudy waterCichlids and sympatric speciation ‘The best example of sympatric speciation in cichlid sh comes, not from the biggest lakes but fiom Lake Barombi Mbo in (Cameroon. This a small ake, only 2.5 km wide, but 110m deep. formed in the crater of a volcano, Only the top 40m contains ‘enough oxygen to sustain vertebrate lie ‘The lake contains 11 species of cichlids. Molecular phylogenetic studies based on both nuclear and mitochondrial DNA show that the species are more closely related to each other than to any other cichlids. What is more, the closest relative of these 11 species is the only cichlid fish found in the streams surrounding the lake, This suggests these fish entered the lake from the streams, perhaps during a rainy season flood, and they have then evolved into 11 different species all in the same small volume of ter, without any geographical barrier between them. They have cevalved to fil different niches, including: + Pungu maclareni, a yellow, blue and black fish that eats a forrn ‘of sponge endemic to the lake + Konia ditume, a deep water fish that can tolerate low axygen and feeds on invertebrates, ‘+ Stomatepia pind, which range from black to purple and feed on other fish + Stomatepia mongo, which has 2 long snout ~it may be a detritivore, Lake Ejagham is another small lake in Cameroon that shows a clear example of sympatric speciation. The lake has a surface area of only 0.5 km? andis 18m deep, but it has a number of different habitats. The bottom of the lake is sandy near the shore, covered with leaves and twigs from the surrounding trees. The lake bo:tom in the middle of the lake is muddy. Lake Ejagham ‘contains two closely related species of cichlids. The smaller species feeds on microscopic animals in the deeper areas of the Jake. The larger species feeds near the edges on invertebrates, including insects that feed on the leaves that fall nto the water near the shore. They breed as well as feed indifferent habitats and 0, although they are in the same tiny lake, they are reproductively jgolated and have formed separate species, Fear for the future ‘The cichlids of the great lakes are valuable in many ways, both as «2 food source for local people and as a tremendous resource for scientists studying the mechanisms of speciation, However, the diversity of the lakes is under threat, In Lake Victoria, Nile perch and water hyacinths were introduced, These changed the ecology the Nile perch is a voracious predator and water hyacinths grow ‘and cover the surface. Deforestation leads to soll erosion so the ‘water has become full of silt nd cloudy. As a result, the cichlids are under threat. Their numbers have been substantially reduced and scientists fear many species will have disappeared before they have been fully identified. Up to two-thirds of the species are now classified as endangered or extinct. Fortunately, sa far the other lakes have fewer problems ~ but for the cichlids of Lake Victoria, itis @ race against time. 0 EE Give examples of isolating mechanisms that lead to (2) allopatricspeciation_(b)_ sympatric speciation 2 coscus the efecto adaptive radlation onthe species ichness ofan ecosystem Lookat the drawings of the Darwin finches. They look very diferent yet are genetically quite simi Explain how this may have come about \Whyare the great lakes of fica such an ideal place to study speciation? ua w Explain how both allopatric and sympatric speciation are involved in the adaptive radiation ofthe cichilid fish ofthe Atican lakes, - Speciation ic the formation of a naw species Hybridisation isthe production of offspring as a result of sexual reproduction between individuals fram two different species. Geographical isolation occurs when a physical barrier such as a river ‘ora mountain range separates ind viduals from an original population. Ecological isolation occurs when two populations inhabit the same region, but develop preferences for different parts ofthe habitat. Seasonal isolation occurs when the timing of flowering or sexual receptiveness in some parts ofa population drifts away from the rnotm forthe group. Ths can eventually lead to the two groups reproducing several months apart, Behavioural isolation happens when changes occur in the courtship ritual, dlsplay or mating pattern so that some animals do not recognise othersas being potential mates. This might be due toa ‘mutation that changes the colour or pattern of markings. ‘Mechanical isolation happens when a mutation occurs that changes the genitalia of animals, making it physically possible for them to imate successfully with only some members ofthe group. ort changes the relationship between the stigma and stamens in flowers, ‘making pollination between some individuals unsuccessful Allopatrc speciation is speciation that takes place when populations are physically or geographically separated and there can be no interbreeding or gene flow between the populations ‘An endemic species isa species that evolves in geographical isolation and is found in only one place. ‘Adaptive radiation sa process by which one species evoles rapidly to forma number efciflerent spaces that al fil dierent ecological riches ‘Marsupials are mammals that give birth to very immature young and then protect them in pouches, ‘Monotremes are primitive mammals that ly eggs and feed their offspring with milk from mammary glands Placental mammals are mammals that provide for the developing Fetus during gestation through a placenta Sympatric speciation is speciation that takes place between populations ofa species ving in the same place. They become reproductively isolated by mechanical, behavioural or seasonal ‘mechanisms and gene flow continues between the populations to some extent as speciation takes place 187REVIVING THE QUAGGA Until recently it was thought thatthe last quagga, a species similar tothe plains zebra, had died in ‘Amsterdam Zoo in 1883, In recent years DNA evidence suggested that the quagga was in fact a sub-species of the plains zebra, and a rebre eding programme in South Africa set out to restore the quagga to the African plains where it belongs. QUAGGA REBREEDING: A SUCCESS STORY taken Loncen Zan 12:05 (GMT#2), Tuesday, April 15, 2014 Until recently, it was believed that the last quagga died in Amsterdam Zo0 in 1883. Today, however, this iconie animal isalive and back in the Western Cape, How was it possible to revive an animal from extinetion? Keri Harvey speaks to the ‘Quagga Project's Craig Lardner. Contrary to popular belief, the quagea Equus quagga quai ‘is nota species in its own right, DNA analysis of quiggn kept fas museum specimens has proven thatthe extinet quagga was in fact a Burchell’s or plains zebra with a colour variation, in which some of its leg and rump stripes disappeared. This also means that a) ‘Bucchell’s or plains zebra still carry genes from the extinet quagea, though these may be more diluted now than before. PN I Te \Where else will! encounter these themes? 188 Vanishing stripes Why exactly the Burchell’s or plains zebra lost some of its stripes is unclear, but. differing colouration seems to provide optimal ‘camouflage: the quagga in each area blend ett into their specific surroundings. Another purported reason for the quag, vanishing stripes, apart from camouflage and hence protection from predators, is tsetse flies. It has been suggested thatthe zebra’s siripes repel tsetse Mles and so 10 the diseases they carry, Because the quugga lived outside the tsetse Ny areas, the distinct stripes became obsolete When it was discovered that the Burchell’s or plains zebra is DNA match for the extinet quagga, the project set about attempting to ‘rebreed’ the quagga. This was done by selecting brownish zebra with reduced stripes and white tail bushes. In this Way, the ‘quagga genes could be concentrated to produce an animal that looks precisely Like the “extinct” quagg. Only mitochondrial DNA was available from museum specimens ‘and not nuclear and living DNA. For this reason, it was impossible to compare the rebred quagga to the original ones that became extinct, Nonetheless, the quagga in the Western Cape are believed to be the “real thing”, as it was in fac pattem that distinguished a quagga from a Burchell’ or plains zebra. Thus the ‘Quagga Project scems 10 have succeeded in rectifying the tragedy that saw them being hunted t0 extinctionie Let us star by looking atthe nature of the writing in this ance. [oowrnese: UrUrrure«nrnny | (Consider she tormat 3 [: Story tod by a joumates feesd on spening ng | soneone trom the Project. we aie | maize you tcl ne, | be nat 7 fale? Was migh nae Yonder if the details / Now let us look at the biology of this amazing story. You know about DNA in cells, classification, \are conect? natural selection and adaptation, Use all of these ideas to help you answer the following questions = ee | / Witing scienticay —~ s YOU read these atticies identity everything that \ crest | | | Sclentic article Foe 2” Acti ty nr a ee || romance toy || Make sire pe a, a eee [Seen setter mitochondrial (mi) DNA sequences from a single quagga (Equus quagga) museum skin..(Higuchiet al Leyes” 11984, Nature 312, 282-284), This was the frst extinct species from which genetic information was retrieved. The DNA sequences of the quagga showed that twas more closely elated to zebras than to horses However, qungga evolutionary history is far from clear We have slated DNA from eight, aquaggas and plans zebra (subspecies or phenotype Equus burchel burchell, We show that the O © cuside of cell Protein carrier returns passively to original shape tw allow more glucose molecules ‘enter ia on Gas fig. Using save wanspon, ci en ieneacetcbemieeton et ‘thecell even when the concentration gradient isin te yrongeinectonee ‘The combination of diffusion, facilitated diffusion and active transport means that the cell surface ‘membrane provides control over what moves into or out of the cell. The concentration of ions ‘and molecules within the cell can be maintained at very different levels from those of the external fluids, In a similar way the membranes around the organelles and in the cytoplasm provide a range of microenvironments within the cell itself each suited to diferent functions, such as the protein. MAE Tslenas endocitoss large particles ~ phagocytosis packaging systems in the Golgi bod. Teds ~ pinocytosis Evidence for active transport ° lps DEG ovsise cat Active transport requires energy inthe form of ATP produced during cellular respiration. Much of y the evidence for active transport comes from linking these two processes together, showing that ‘without ATP active transport cannot take place: 1. Active transport takes place only in living, respiring cells, 2. The rate of active transport depends on temperature and oxygen concentration. These affect the rate of respiration and so the rate of production of ATP. 3. Many cells that are known to carry out a lot of active transport contain very large numbers of mitochondria - the site of aerobie cellular respiration and ATP production 4 Poisons that stop respiration or prevent ATPase from working also stop active transport, For example, eyanide prevents the synthesis of ATP during cellular respiration, It also stops active ene craaport However if ATP added arial act wenspor start agen eee exocytosis Endocytosis and exocytosis fg The properties of hecel Difsion and active teansport allow the movement of small pariles across membranes. However, [aoe ther are tmes when larger patties ned io enter or leave a cel for example when white bood ime cells ingest bacteria or gland cells secrete large steroid hormones, Membrane transport systems ‘cannot do this job, but the membrane has properties that make it possible to move larger particles into or out of the cell. Materials can be surrounded by and taken up into membrane-bound vesicles in a process known as, endocytosis (900 fig B). This can oceur ata telaively large seale, for example during the ingestion of bacteria during phagocytosis (cell eating), It also happens at a microscopic level, when tiny’ ‘amounts of the surrounding fluid are taken into minute vesicles. This is known as pinocytosis (cell drinking). Electron microscope studies have shown that pinocytosis is very common as cells take in the extracellular fluid as a source of minerals and nutrients. Exocytosis is the term for the emptying of a membrane-bound vesicle at the surface of the cell ar elsewhere (see fig B). For example, in cells producing hormones, vesicles containing the hormone fuse with the cell surface membrane to release their contents, These processes are made possible by the fuid mosaic nature of the feces mand ty cic ‘membrane, The formation of vesicles and the fusing of vesicles with the surface cell membrane are coll membrane both active processes, requiring energy supplied by ATE, pinocytosis 1 exphin tneimportance of ative warsort incl 2 disasstherolof AP inactive rarspotin the cel 3- suggest how endoctsis and exocytosis prod evidence othe tid mosaic model of membranes. Key definitions Cartier proteins are proteins that movea substance through the membrane in active transport = usualy linked to an ATPase to break down ATP. Cyanide isa metabolic polzon that stops mitochondria working. Phagocytosis is the active process when cell engulfs something relatively large such asa bacterium and encloses tin a vesicle Pinocytosis isthe active process by which cells take tiny amounts of extracellular fluid into vesicles. 221ce 1 (a) Describe the structure of the cell surface (plasma) membrane. (51 (b) The ability of a substance to pass into a cell depends cn its solubility n oil and water The oi-water partition coefficient is a measure of the solubility of a substance in cil compared to water The equation below shows how itis calculated. g a __ Solubility in Oitwater partition coeiient = wae ‘The graph below shows the relationship between, membrane permeability and the oil-water partition ccoeflcient forfour different substances A, B, Cand D, 10: Membrane permeabilty/ ‘arbitrary units o 05 040 (Oit-water partition coefficient (0) Compare and contrast the ability of substances A, B, C and D to cross a cell surface membrane. (3) (i) Using the information shown in the graph and your knoviledge ofthe cell surface membrane, explain how substance A erosses a membrane. [3] (Total: 11] 2. The diagram below represents the structure ofthe cell surface ‘membrane AKO (a) Explain why the phospholipid molecules form a bilayer (3) (b) A student carried out an experiment to investigate the effect of aleahol concentration on the permeability of beetroot membranes. Exam-style questions Beetroots are root vegetables that appear red because the ‘vacuoles in their cells contain a water-soluble red pigment This pigment cannot pass through membranes, Eight pieces of beetroot were cut. One piece of beetroot was placed into a tube containing 15 cm’ of water and left for 15 minutes. The procedure was repeated for seven different concentrations of ethanol, After 15 minutes, each piece of beetroot was temoved fiom the tubes and a sample of the fluid removed and placed in a colorimeter. The colorimeter ‘was used to determine the intensity of red coloration of the fui ‘The results ofthe investigation are shown in the graph below. Intensity of red coloration’ axbitrary units °O 10 20 30 40 50 60 70 ‘Concentration of ethanol % {i) Name two variables, other than those stated above, ‘which should be kept constant during this experiment. 2) {i) There was some red coloration in the tube containing only water. Give an explanation for this. 2 (i) Deseribe whet the student should have done to reduce the red coloration inthe tube containing only water. [1] (c) The graph above shows that ethanol has an effect on the permeability of beetroot. (i) State the effect thatthe ethanol concentration hes on the intensity of the red coloration. 0) {i) Give an explanation for this effect. 2) [otal: 11] 13. Molecules are transported into and out of cells by several ‘mechanisms. (a) Read through the following passage that describes sore of these mechanisms, then write on the dotted lines the most appropriate word or words to complete the passage. [4] Some molecules move across a cell surface membrane by passing down a concentration gradient, through the phospholipid bilayer ‘The movement of some polar molecules across the membrane involves carrier and channel ‘molecules. When this movement occurs dewn a concentration gradient,the process is called and when it occurs against a concentration gradient the process is called Energy in the form of is usedin the movement of molecules against @ concentration gradient, A student wanted to sweeten some strawberries, so she sprinkled some sugar on tap of them, one hour before cating them. The student noticed that the sugar that she had sprinkled on them was no longer visible and that there was some juice at the bottom of the bowl, , — i ‘The student thought that the juice was the sugar dissolved 5 in water and that the water had come from the fru. In order to test this hypothesis, she weighed some fresh straviberries and sprinkled them with sugar. One hour later she rinsed off the juioe and reweighed the strawberries. The rmass of the strawberries before adding the sugar was 77 g ‘The mass ater rinsing off the juice was 70g () Calculate the percentage decrease in the mass of the strawberries. Show your working rl (i) Identify one possible source of error in the student's procedure that could make this value for the percentage decrease in the mass of the strawberries inaccurate. Explain how this source of error would affect the value for the percentage decrease in the mass of the strawberries Bi) (ii) Using your knowledge of cell transport mechanisms and the properties of water explain how the juice is formed from the water that care from the fruit. [3] [Total: 12] 4 Amoeba's a single-celled aquatic organism. Substances in the ‘water can enter the cell by a variety of mechanisms, ‘An experiment was carried out to compare the uptake into Amoeba of substance A and substance B. Some of these organisms were placed in a solution containing ‘equal concentrations of both substances and kept at 25°C. The ‘concentration of substances A and B, in the cytoplasm of these ‘organisms, was measured every 30 minutes over a period of § hours. ‘The results of this experiment are shown in the graph at the top of the next column. 1 Substance A BES 0 BG aa s Ese substance B ore a rn a3 Time/hours| (2) Using the information in the graph. compare and contrast, the uptake of substance A with the uptake of substance B during this period of 5 hours. ia] (b) Substance B enters the cells by diffusion. Explain how the results of this experiment support this statement. (4) (c) Substance A enters the cals by active transport. Give two differences between active transport and diffusion. [2] (Total: 9} Substances are moved in and out of cells by diffusion and active anspor. (2) Explain how molecules move by diffusion 2) (0) The graph below shows the changes in concentration of substance A on the inside and outside of a partially permeable membrane, during a 50 minute period. 100: outside the partialy permeable nembrane ial permeabie nembrane inside the partaly pereable embrane io 2 30 430 Timne/min Substance A crosses from one side ofthis membrane tothe other by diffusion, Describe how the information given in the graph supports this statement. 3] (c) () Give two differences between diffusion and active transport. 1 (i) Describe how the changes in concentration of substance A would differ if active transport were used to transfer substance A acrass the membrane. [2] (Total: 9}